Jussieu was born into a family of eminent botanists from Lyons in France. His uncles Antoine, Bernard, and Joseph de Jussieu all made important contributions to botany and his son, Adrien, subsequently continued the family tradition.

After graduating from the Jardin du Roi in 1770, Jussieu continued to work there, becoming subdemonstrator of botany in 1778. In his first publication in 1773, which reexamined the taxonomy of the Ranunculaceae, he advanced the idea of relative values of characters; the following year he applied this principle to other plant families.

Jussieu is remembered for introducing a natural classification system that distinguishes relationships between plants by considering a large number of characters, unlike the artificial Linnean system, which relies on only a few. In producing the famous Genera Plantarum (1789; Genera of Plants) Jussieu had access to a number of collections, including Linnaeus's herbarium and some of Joseph Banks's Australian specimens. He was also able to include many tropical angiosperm families thanks to the collection made by Philibert Commesson. From all this material he distinguished 15 classes and 100 families, and the value of his work can be seen in the fact that 76 of his 100 families remain in botanical nomenclature today. Both Georges Cuvier and Augustin de Candolle built on Jussieu's system.

Jussieu was in charge of the hospital of Paris during the French Revolution and was professor of botany at the National Natural History Museum (formerly the Jardin du Roi) from 1793 to 1826.