In the midst of much upheaval, the Manchus seized control of Beijing in June 1644, and in October of the same year the Shunzhi emperor's uncle, the chief regent Prince, proclaimed the Qing dynasty to be the legitimate successor to the Ming Dynasty. Therefore, although the Shunzhi emperor was not the founder of the Qing dynasty, he was the first Qing emperor of China.

One of Dorgon's most controversial decisions was his 1646 imperial edict (the "Queue Order") which forced all Han Chinese men, on pain of death, to adopt the Manchu style of dress, including shaving the front of their heads and combing the remaining hair into a queue. To the Manchus this policy might both be a symbolic act of submission and in practical terms an aid in identification of friend from foe, however for the Han Chinese it went against their traditional Confucian values. Unsurprisingly, it was deeply unpopular and, together with other policies unfavourable towards the Han Chinese, might account for the increasingly steep resistance met by Qing forces after 1646. Hundreds of thousands of people were killed before all of China was brought into compliance.

His mother was the Empress Dowager Xiaozhuang who was an excellent politician during the period. The young emperor disliked his uncle, the chief regent Prince Dorgon, and after Emperor Chengzong's (posthumous title) death in 1650 the emperor stripped both him and Dorgon's brother, Dodo, of their titles and assumed full imperial authority.

During his short reign, the Shunzhi emperor encouraged the Han Chinese to participate in government activities. He was a scholar and employed Han Chinese to teach his children. He was also an open minded emperor and relied on the advice of Johann Adam Schall von Bell 湯若望, a Jesuit from Germany, for guidance ranging from astronomy, technologies, to tips for governing an empire. Shunzhi also elevated Schall to his personal mentor and was given free access to the palace.

The emperor married his mother's niece, but demoted the empress several years later. In 1661, Shunzhi's favourite concubine Donggo suddenly died as a result of grief over the loss of a child. Overwhelmed with grief himself, Shunzhi contracted smallpox and died shortly thereafter. Before he died, he appointed four regents to govern for his child son, Xuanye - Oboi, Sonin, Suksaha, and Ebilun.

According to official sources, the Shunzhi Emperor died in 1661 of smallpox. It was also believed by some that the young emperor did not pass away but left the palace to become a monk. He was interred in the Eastern Qing Tombs (清東陵), 125 kilometers / 75 miles east of Beijing, in the Xiaoling (孝陵) mausoleum complex (known in Manchu as the Hiyoošungga Munggan).

Hong Taiji had changed the name of the dynasty from Later Jin to Qing in 1636 because of the fraternal struggles and skirmishes between brothers and half brothers for the throne. According to Taoist philosophy, the name Jin has the meaning of metal and fire in its constituent, thereby igniting the tempers of the brothers of the Manchu Royal household into open conflicts and wars. Huangtaiji therefore adopted the new name of Qing 清, the Chinese character of which has the water symbol [3 strokes] on its left hand side. The name, which means clear and transparent, with its water symbol was hoped to put out the feud among the brothers of the Manchu Royal household.

Because of power issues in the Qing's ancestors' way, Shunzhi ultimately took another step to consolidate the power of the emperor. According to the old way, the 8 Banners were passed with succession much like how Nurhaci decided to give his Yellow Banners to Dorgun, but could potentially be controlled by someone like Huang Taji who switched the Banners. To solve this problem, Shunzi ordered the Upper 3 Banners - Plain Yellow, Striped Yellow, and Plain White to be under the control of the emperor. This would be maintained until Yongzheng and Qianlong's reign when they took the last step and controlled all 8 Banners.

It's also noteworthy that the empire was generally clean from corrupt officials as Shunzhi despised corrupt officials.

Information is not clear, but it is said that Shunzhi later become a monk. Although not officially stated in history, it is said he later died of smallpox. He was later erased from history shortly after his death.

Shunzhi was buried in what later came to be known as the "Eastern Qing Tombs" northeast of Beijing, one of two Qing imperial cemeteries.