Little is known about interactions of iron with temperature, light, nitrate and ammonium on physiology of the freshwater species Microcystis aeruginosa (Cyanobacteria). Results showed that growth and photosynthesis of M. aeruginosa were inhibited by Fe limitation in all cultures beside nitrogen-treatment groups. Relatively low or high temperature and light intensity could impair the growth and photosynthesis of M. aeruginosa despite Fe concentration in media. Under Fe-replete conditions, both the OD665 and chlorophyll a reached peaks at 30 °C and light intensity of 30 μmol photons m-2 s-1. Nitrate is proven to be the main nitrogen source for growth of M. aeruginosa collected from Lake Dianchi. Yield, ETRmax, α and Ik also reached highest values at light intensity of 30 μmol photons m-2 s-1 and high FeNO3- conditions, but at a temperature of20 °C. Our results can be used to help control blooms of M. aeruginosa in Lake Dianchi and other water-bodies.