Wind-driven wave disturbance is one of the environmental factors that shapes the formation of Microcystis blooms. Here we present data on the effect of different disturbance modes (continuous vs intermittent disturbances) on colony size, biomass and dominance of Microcystis in Lake Taihu under field conditions. Small submersible pumps were used to simulate different disturbance modes at turbulent dissipation rate (ε) of 2.98 × 10-6 m2 s-3. Our results show that the mean colony sizes of Microcystis in intermittent and continuous disturbance group were 1.94 and 1.23 times that of the control group, respectively. The mean densities of Microcystis in intermittent and continuous disturbance group were 4.23 and 2.91 times that of the control group, respectively. The mean proportion of Microcystis to total algae abundance in control group and continuous disturbance group changed from 78.3% at beginning of the experiment to 4.5% and 9.1% at the end of the experiment. However, the proportion of Microcystis to total algae cells in intermittent disturbance group was 65.7-94.3% during the whole experiment. The results demonstrated intermittent disturbances favored colony morphology, biomass and dominance of Microcystis. Our results suggested that intermittent disturbance benefited the formation of Microcystis bloom and was important in the development of predictive models for toxic cyanobacterial blooms under changing climates in shallow lakes.