In 1712 the Kangxi Emperor removed his second son, Yinreng, as successor to the throne and did not designate another one. This led to further division in Court, which was long split among supporters of Yinzhi, Yinzhen, Yinsi, and Yinti, the 3rd, 4th, 8th and 14th Imperial Princes, respectively. Of the princes, Yinsi had the most support from the mandarins, though often for self-serving reasons. Prior to this, Yinzhen had supported the Crown prince. When the Emperor died in December 1722, the field of contenders had been reduced to three Princes after Yinsi pledged his support to the 14th prince Yinti (Yinzhen's brother by the same mother).

At the time of the Kangxi Emperor's death, Yinti, as Border Pacification General-in-chief (撫遠大將軍), was at the warfront in the northwest. Certain historians say this was to train the next Emperor in military affairs; others maintain that it was to ensure a peaceful succession for Yinzhen. It was Yongzheng who nominated Yinti for the post, and not Yinsi, whom Yinti was closely affiliated with. This post was seen as an indication of Kangxi's choice of successor, as the position of Crown Prince had been vacant for 7 years.

The official record, which could have been modified by Yongzheng himself for political purposes, states that on 20 December 1722, the ailing Kangxi Emperor called seven of his sons and the General Commandant of the Peking Gendarmerie, Longkodo, to his bedside, who read out the will and declared that Yinzhen succeed him on the imperial throne. Some evidence have suggested that Yinzhen had contacted Longkodo months before the will was read in preparation for succession by military means, though in their official capacities, frequent encounters were only to be expected. Folklore has it that Yongzheng changed Kangxi's will by adding strokes and modifying characters. The most famous account says Yongzheng changed fourteen (十四 → shísì) to "to four" (于四 → yúsì), others say it was fourteen to fourth (第四 → dìsì). Whilst widely circulated, there is little supporting evidence, especially considering that the character "于" was not widely used during the Qing Dynasty, i.e., on official documents, "於" (yú) is used. Secondly, Qing tradition insists that the will was done in both Manchu and Chinese, and Manchu writing is much harder, and in this case impossible to modify. Furthermore, princes in the Qing Dynasty are referred to as the Emperor's son, in the order which they were born. (Ex.: "The Emperor's Fourth Son" Chinese:皇四子) Therefore, there are much doubt to the theory of Yinzhen changing the will to ascend to the throne.

Yinzhen chose an era name that was similar in sound to his given name, and 1723 was to be the first year of the Yongzheng era. As the first official act as emperor, Yongzheng released his long time ally, the 13th prince Yinxiang, who had been imprisoned by the Kangxi Emperor at the same time as the Crown Prince. Some sources indicate that Yinxiang, the most military of the princes, then assembled a group of special task Beijing soldiers from the Fengtai command to seize immediate control of the Forbidden City and surrounding areas, to prevent any usurpation by Yinsi's cronies. Yongzheng's personal account stated that he was emotionally unstable and deeply saddened over his father's death, and knew it would be a burden "much too heavy" for himself if he were to succeed the throne. In addition, after the will was read, Yinzhen wrote that the officials (premier Zhang Tingyu, Longkedo and Yinzhi) and the Prince Cheng led the other Princes in the ceremonial Three-kneels and Nine-Salutes to the emperor. On the next day, Yongzheng gave out an edict summoning Yinti back from Qinghai, bestowing upon their mother the title of Holy Mother Empress Dowager the day Yinti arrived at the funeral.

In the first major comprehensive biography of the Yongzheng Emperor by Feng Erkang, the author put the Yongzheng succession in perspective. Feng wrote that there were some suspicious signs from the lost wills and the dates released, but the majority of evidence points to Yinzhen succeeding the throne legitimately, albeit with some political and military manoeuvering deemed necessary by the situation. The 8th prince Yinsi had throughout his life been amassing support of the officials by bribery, and his influence had penetrated the Fengtai command. Furthermore, Feng suggested "although we are not yet altogether certain on what happened with the succession, and which side is correct, it is reasonable to think that Yongzheng's political enemies manipulated all suspicion behind the will in an attempt to put a dark image on Yongzheng; Imperial Chinese tradition had led certain schools of thought in believing that Yongzheng's whole reign can be discredited simply because his succession of the throne did not come as a will of his father, the emperor and ultimate decision maker in China." He further suggested that Kangxi had made a grave mistake by letting his sons become major players in politics, especially under the condition that the position of Crown Prince was empty, and that a bloody battle of succession, including a possible usurpation, is the inevitable result of the Imperial Chinese institution and history. Therefore it would be an even bigger mistake to judge a ruler solely on the way he came to power. Certainly, the Yongzheng Emperor made sure that his successor would have a smooth succession when his turn came.

In December 1722, after succeeding to the throne, Yinzhen took the era name of "Harmonious Justice" (雍正 → yōngzhèng), effective 1723, from his peerage title "harmonious" (雍 → yōng) and "just, correct, upright" (正 → zhèng). It has been suggested that the second character of his era name was an attempt to cover up his illegal claim to the throne, calling himself "justified". Immediately after succeeding the throne, Yongzheng chose his new governing council. It consisted of the 8th prince Yinsi, the 13th prince Yinxiang, Zhang Tingyu, Ma Qi, and Longkodo. Yinsi was given the title of Prince Lian, and Yinxiang was given the title of Prince Yi, both holding the highest positions in the land.

As the nature of his succession is deeply clouded, Yongzheng saw a challenge in all his surviving brothers. Yinzhi, the eldest, continued to live under house arrest and Yinreng, the former Crown Prince, died two years into his brother's reign - though they were both imprisoned, not by Yongzheng, but by Kangxi himself. The biggest challenge was to separate Yinsi's party (consisting of Yinsi and the 9th and 10th princes, and their minions), and isolate Yinti to cut their dominance. Yinsi, who had nominally held the position of President of the Feudatory Affairs Office, the title Prince Lian, and later the office of Prime Minister, was held under close watch by Yongzheng. Yintang was sent to Qinghai under the pretext of military requirement, but in reality fell within Yongzheng's trusted protégé Nian Gengyao's territory. Yin'e, the 10th Prince, was rid of all his titles in May 1724, and sent north to the Shunyi area. The 14th Prince Yinti, his brother born to the same mother, was placed under house arrest at the Imperial Tombs, under the pretext of watching over their parents' tombs.

The first few years of Yongzheng's reign saw an increase in partisan politics. Yinsi had wanted to use his position to manipulate Yongzheng into making wrong decisions, while appearing supportive. Yinsi and Yintang, both supporters of Yinti for the throne, had all of their titles rid, languished in prison and died in 1727.

Nian Gengyao was a supporter of Yongzheng long before he succeeded the throne. In 1722, when he was summoning back his brother Yinti from the northwest, he appointed Nian to fill in the position. The situation in Xinjiang at the time was still very much precarious, and a strong general was needed in the area. After several military conquests, however, Nian Gengyao's greed for power grew. Nian reputedly wanted to be level to Yongzheng himself. Seeing the situation unfold, Yongzheng issued an Imperial Edict demoting Nian to the general of the Hangzhou Command. Continuing to be unrelenting of his outlook, Nian was given an ultimatum, after which he committed suicide by poison in 1726. Longkodo was commander of Beijing's armies at the time of Yongzheng's succession. He fell to disgrace in 1728 and died while under house arrest.

After he became emperor, Yongzheng suppressed writings that he deemed unfavorable to his regime, particularly those with an anti-Manchu bias. Foremost among these was the case of Zeng Jing, a failed degree candidate heavily influenced by the seventeenth century scholar Lü Liuliang. Zeng had been so affected by what he read that he attempted to incite Governor general of Shaanxi - Sichuan, Yue Zhongqi to rebellion. The general promptly turned him in, and in 1730 the case reached Yongzheng Emperor. Highly concerned with the implications of the case, Yongzheng had Zeng Jing brought to Beijing for trial. The emperor's verdict seemed to be an exhibition of the benevolence of the Confucian sovereign: He ascribed Zeng's actions to the gullibility and naivety of youth, taken in by Lü's abusive and overdrawn rhetoric. In addition to this, the emperor suggested that Lü's own original attack on Manchus was misplaced because the Manchus had been transformed by their long term exposure to the civilizing force of Confucianism.

Yongzheng is also known for establishing strict autocratic rule in the time period. He disliked corruption and punished officials severely when they were found guilty of the offence. In 1729, he gave an edict prohibiting the smoking of madak, a blend of tobacco and opium. During Yongzheng's reign, the Manchu Empire became a great power and a peaceful country, and he furthered strengthened the Kangqian Period of Harmony (康乾盛世). He created a sophisticated procedure for selecting successor in response to his father's tragedy.

Yongzheng was known for his trust in Mandarin Chinese officials. Li Wei and Tian Wenjing were both used to govern China's southern areas. Ertai also served Yongzheng's in governing the southern areas.

Like his father, Yongzheng used military force in order to preserve the dynasty's position in Outer Mongolia. When Tibet was torn by civil war during 1727 - 28, he intervened militarily. Upon intervention, he left behind a Qing resident (the amban) backed up by a military garrison to pursue the dynasty's interests. For the Tibetan campaign, Yongzheng sent an army of 230,000 led by Nian Gengyao against the Dzungars who had an army of 80,000. Due to the geographic reasons, the Qing army though vastly superior, couldn't engage the mobile enemy. Eventually, the Qing engaged the enemy and defeated it. This campaign cost the treasury at least 8,000,000 taels of silver. Later in Yongzheng's reign, he would send another small army of 10,000 to fight the Dzungars. However, the whole army was completely annihilated, the Qing Dynasty nearly lost control of the Mongolian area. Luckily, a Qing ally, the Khalkha tribe would defeat the Dzungars.

Overall, after the reforms of 1729, the treasury increased from 1721 of 32,622,421 taels to about 60,000,000 taels in 1730, surpassing the record set during Yongzheng's father, Kangxi Emperor's regime; however, the pacification of the Qinghai area and the defense on the borders area was a heavy burden. Just for the borders, 100,000 taels was needed each year. The total military cost added up to 10,000,000 taels a year. By the end of 1735, military spending have used up half of the treasury and the treasury rested at 33,950,000 taels. It is because of this heavy burden that Yongzheng Emperor considered making peace with the Dzungars.

The Yongzheng Emperor ruled the Qing Empire for thirteen years before dying suddenly in 1735 at the age of fifty-eight. Legend holds that he was assassinated by Lü Siniang, daughter of Lü Liuliang, whose family was (reportedly) executed for literary crimes against the Manchu Regime. Another reason had been that Lü was the real mother of Qianlong but Yongzheng did not allow Lü to be the Queen. In actual fact it is likely his death was a result of an overdose of the medication he was consuming that he believed would prolong his life.

Yongzheng Emperor's family life seems relatively sad. Of the fourteen children born to him and his Empresses and concubines, only five are known to have survived to adulthood. To prevent the succession tragedy he faced, he ordered his third son, Hongshi, who had been an ally of Yinsi, to commit suicide. His son Hongli, the Prince Bao, then became the fifth emperor of the Qing dynasty under the era name of Qianlong.

Yongzheng Emperor was interred in the Western Qing Tombs (清西陵), 120 kilometers - 75 miles southwest of Beijing, in the Tailing (泰陵) mausoleum complex (known in Manchu as the Elhe Munggan).