Disturbance induced by wind-wave is one of the important environmental factors that affect the lake ecosystem. To understand the effect of disturbance modes on the size of Microcystis flos-aquae colonies in lakes, one experiment on the effects of different simulated disturbance modes (continuous disturbance and intermittent disturbance) on the size of Microcystis flos-aquae colonies from Lake Taihu was conducted under controlled conditions in laboratory. The experiment results showed that the size of Microcystis flos-aquae colony increased rapidly from 35.09 μm to 43.73 μm in the intermittent disturbance groups, and to 59.00 μm on the 17th day of the experiment. However, the size of Microcystis flos-aquae colony in the continuous disturbance groups increased from 35.07 μm to 43.51 μm, and decreased to 13.95 μm on the 17th day of the experiment. The size of Microcystis flos-aquae colony in the non-disturbance groups was relatively stable throughout the experiment, which was 35.38 μm, 33.67 μm at the beginning and on the 17th day of the experiment, respectively. Variance analysis showed that the size of Microcystis flos-aquae colony in the intermittent disturbance groups was significantly greater than that in the continuous disturbance groups and the non-disturbance groups. Also, the size of Microcystis flos-aquae colony in the continuous disturbance groups was significantly smaller than that in the non-disturbance group. On the 17th day of the experiment, the algal cell density (1.675×10⁶ cells/ml) was significantly higher in the intermittent disturbance groups than that in the continuous disturbance groups (0.344×10⁶ cells/ml) and the non-disturbance groups (1.461×10⁶ cells/ml). The results showed that intermittent disturbances at appropriate intensities could significantly increase the size and the growth of Microcystis flos-aquae colony, but continuous disturbance could inhibit their aggregation and growth over long time, which is valuable for understanding the breakout mechanism of Microcystis blooms in Lake Taihu.