Mixing is an integral environmental factor that affects lake ecosystems. For the cyanobacterium Microcystis, colony size is important with respects to migration velocity, how cells respond to grazing pressure, light attenuation, nutrient uptake and growth. To understand how mixing shapes colony size and the growth of Microcystis, we measured the effects of different current velocities (0, 0.16, 0.32, 0.64, and 1.28 m s−1) on M. aeruginosa in Lake Taihu. After 24 h of continuous mixing, the mean colony sizes of M. aeruginosa in the controls, 0.16, 0.32, 0.64, and 1.28 m s−1 groups were 23.6, 50.1, 92.9, 67.8, and 37.3 μm, respectively. Colony sizes of M. aeruginosa in all treatment groups were significantly larger than those in controls. As well, the concentration of soluble extracellular polysaccharide and bound extracellular polysaccharides of M. aeruginosa in all treatment groups were significantly higher than those in controls. Except for the highest level of mixing (1.28 m s−1), the growth rate of M. aeruginosa was significantly higher than that in controls. This study suggested that mixing intensity over short time periods can significantly influence colony size and the growth of M. aeruginosa.