Malus, who was born in Paris, attended the military school in Mezières (1793) and the newly established Ecole Polytechnique (1794–96) where he received his basic scientific education. He was commissioned in 1796 and served as a military engineer in Napoleon's expedition to Egypt and Syria. After his return to France he held various military engineering appointments. He became an examiner in geometry and analysis in 1805 and an examiner in physics in 1806 at the Ecole Polytechnique; these posts brought him into contact with other physicists.

Malus carried out many researches in optics, which was his main scientific interest. He is remembered for his discovery made in 1808 that light rays may be polarized by reflection. He found this while looking through a crystal of Iceland spar at the windows of a house reflecting the rays of the Sun; he noticed that on rotating the crystal the light was extinguished in certain positions. In explaining his observations Malus, a Newtonian and believer in corpuscular theory, argued that light particles have sides or poles and used for the first time the word ‘polarization’ to describe the phenomenon.

Malus's work in optics gave considerable impetus to investigations into polarization and the optical properties of crystals.