Abstract: In order to investigate the effects of indole-3-acetic acid (IAA) on physiological characteristics of Microcystis aeruginosa (M. aeruginosa), the growth, photosynthetic pigment content, chlorophyll fluorescence, lipid oxidation, and microcystin biosynthesis characteristics were studied. The achieved results showed that there was no significant variation in cell density, chlorophyll content, chlorophyll fluorescence characteristics, and microcystin contents at low concentrations of IAA (e.g., 0.04 and 0.2 mg/L). However the contents of phycocyanin, allophycocyanin, and malondialdehyde (MDA) decreased in comparison with the control group. High concentrations of IAA (1 and 5 mg/L) accelerate the algal growth and increased chlorophyll content, while that inhibited the contents of phycocyanin and allophycocyanin and reduced the peroxidation of membrane lipid peroxidation as well as synthetization of intracellular algal toxins. The findings also demonstrated that low concentrations of IAA have no clear influence on the growth and photosynthesis of M. aeruginosa CHAB-6301. However, high concentrations of IAA can promote the growth and photosynthesis of this alga, which may increase the possibility of formation of Microcystis-based water blooms.