The formation and accumulation of massive Microcystis colonies was an important prerequisite in Microcystis blooms formation. Light intensity was an essential ecological factor affecting the growth of Microcystis. To understand the effect of light intensity on growth of Microcystis colonies size, a study was conducted on the effect of different light intensity on the colony size growth of Microcystis flos-aquae which was one of the dominant species of Microcystis bloom in Lake Taihu. In this study, five different light intensity treatments were set up as follows:G1:2000 lx; G2:4000 lx; G3:8000 lx; G4:16000 lx; G5:change light (simulating light intensity changes in the field). During the experiment, the average size of colony (above 100 cells) of M. flos-aquae in G1-G5 were 255, 480, 630, 763 and 662 cells/colony, respectively. The analysis of extracellular polysaccharides showed that extracellular polysaccharides concentration increased with the increase of M. flos-aquae colony size. Our results showed that low light intensity was disadvantage for the growth of M. flos-aquae colony size. However, high light intensity and variation of light intensity were advantage for the growth of M. flos-aquae colony size. This study explained why light intensity changed in the field and high light intensity were in favor of the formation of Microcystis bloom in summer in Lake Taihu.