During his stay at Rostock, he became an early follower of the antiphlogistic theory of Lavoisier, teaching about the existence of oxygen instead of phlogiston.

He began to write an abundant number of articles and books on the most different subjects, such as physics and chemistry, geology and mineralogy, botany and zoology, natural philosophy and ethics, prehistoric and early history.

During 1797–1799, he visited Portugal with Count Johann Centurius Hoffmannsegg, a botanist, entomologist and ornithologist from Dresden.

After the death of Carl Ludwig Willdenow in 1815, he became professor of natural history, curator of the herbarium and director of the botanic garden (Hortus regius Berolinensis) in Berlin until he died.

Link was also one of the few German botanists of his time, who aimed at a complete understanding of plants, through a systematic anatomical and physiological research.

His most important work is the Handbuch zur Erkennung der nutzbarsten und am häufigsten vorkommenden Gewächse (three volumes, published between 1829 and 1833).