Hevelius' father was Abraham Hewelke (1576 – 1649), his mother Kordula Hecker (1576 – 1655). They were a German-speaking family of wealthy brewing merchants of Bohemian origin. Hevelius brewed the famous Jopenbier, which also gave its name to Danzig's Jopengasse, the street where St. Mary's church is located.

After gymnasium, where he was taught by Peter Crüger, Hevelius in 1630 studied jurisprudence at Leiden, then traveled in England and France, meeting Pierre Gassendi, Marin Mersenne and Athanasius Kircher. In 1634 he settled in his native town, and on March 21, 1635, married Katharine Rebeschke, a neighbor two years younger who owned two adjacent houses. The following year, Hevelius became a member of the beer-brewing guild, which he led from 1643 onwards. There is a modern popular beer named after his brewing style, Hevelius Kaper.

Throughout his life, Hevelius took a leading part in municipal administration, becoming Ratsherr (town councillor) in 1651; but from 1639 on, his chief interest was astronomy. In 1641 he built an observatory on the roofs of his three connected houses, equipping it with splendid instruments, including ultimately a large Keplerian telescope of 45 m (150 ft) focal length, with a wood and wire tube he constructed himself. This may have been the longest "tubed" telescope before the advent of the tubeless aerial telescope. This private observatory was visited by Polish Queen Maria Gonzaga on 29 January 1660, and in 1678 by Polish King John III Sobieski. In May 1679, the young Englishman Edmund Halley visited him as emissary of the Royal Society. Since 1664 Hevelius was its first German member (fellow). Małgorzata Czerniakowska believes that "Jan Heweliusz was the first Pole included among the members of the Royal Society in London. This important event took place on 19th March 1664".

Halley had been instructed by Robert Hooke and John Flamsteed to persuade Hevelius to use telescopes for his measurements, yet Hevelius demonstrated that he could do well with only quadrant and alidade. He is thus considered the last astronomer to do major work without the use of a telescope. Hevelius made observations of sunspots, 1642 – 1645, devoted four years to charting the lunar surface, discovered the Moon's libration in longitude, and published his results in Selenographia, sive Lunae descriptio (1647), a work which entitles him to be called "the founder of lunar topography."

He discovered four comets, in 1652, 1661 (probably Ikeya-Zhang), 1672 and 1677. These discoveries led to his thesis that such bodies revolve around the Sun in parabolic paths.

A Halophänomen was observed by many in Danzig and described by Hevelius to pastor Georg Fehlau of St. Mary's church, titled Siebenfältiges Sonnenwunder oder sieben Nebensonnen, so in diesem 1661 Jahr den 20. Februar neuen Stils am Sonntage Sexagesima um 11 Uhr bis nach 12 am Himmel bei uns sind gesehen worden.

Katharine, his first wife, died in 1662, and a year later Hevelius married Elisabeth Koopmann, the young daughter of a merchant family. The couple had four children. Elisabeth supported him, published two of his works after his death, and is considered the first female astronomer.

His observatory, instruments and books were maliciously destroyed by fire on September 26, 1679. The catastrophe is described in the preface to his Annus climactericus (1685). He promptly repaired the damage, so far as to enable him to observe the great comet of December 1680. He named the constellation Sextans in memory of these lost instruments. His health had suffered from the shock, and he died on his 76th birthday, January 28, 1687. Hevelius was buried in St. Catherine's Church in Danzig.

In late 1683, in commemoration of the victory of Christian forces led by King John III Sobieski at the Battle of Vienna, he had discovered and named the constellation Scutum Sobiescianum (Sobieski's Shield), now called Scutum.

Hevelius had his book printed in his own house, at lavish expense, and himself engraved many of the printing plates.

A memorial plaque where he held office at the Rathaus in Danzig (city hall), reads DEM ANDENKEN DES JOHANNES HEVELIUS ASTRONOM V RATSHERR DER ALTSTADT GEBOREN AM 28 JAN 1611 - GEST. AM 28 JAN 1687.