Cyanobacterial bloom is one of the most urgent global environmental issues, which eventually could threaten human health and safety. Sonication treatment (ST) is a potential effective method to control cyanobacteria blooms in the field. Currently, the bottleneck of extensive application of ST is the difficulty to estimate the ST effect on the cyanobacterial cells and then determine suitable ST times in the field. In this study, cyanobacterial Microcystis samples sonicated at different times were first measured by a spectrophotometer to calculate the removal efficiency of Microcystis cells. Additionally, they were observed by TEM to reveal the intracellular structure changes of the cells. Then the samples were measured by an experimental setup based on polarized light scattering to measure the polarization parameters. Experimental results indicated that the polarization parameters can effectively characterize the intracellular structural changes of Microcystis cells with different ST times, which is quite consistent with the results for removal efficiency and TEM images. Further, the optimal ST time can be inferred by the polarization parameters. These results demonstrate that polarized light scattering can be a potentially powerful tool to explore suitable times for sonication treatment of cyanobacteria blooms.