Microcystis present as colonies in natural environment, which make it difficult to calculate Microcystis cells number. This paperexplored the disruption of Microcystis in different ultrasonic power and treatment time, and Microcystis cells number was quantified by CytoSenseand EasyClus. The experimental results show that with the increase of ultrasonic power and treatment time, the effect of dispersion improved firstand then decreased. The number of Microcystis particles and the total value of red fluorescence reached the highest after 96 s ultrasonic treatment(480W), at the same time, FWS forward scattering value reached minimum, and Microcystis cells were disrupted. Also under 480W, with theincrease of treatment time, more Microcystis cells were disruped. Therefore, it was determined that the optimal ultrasonic dispersion power forMicrocystis colonies was 480W, and the optimum treatment time was 72s. The results of microscopy counting and EasyClus analysis show that thismethod is accurate and and efficient, which can be used for rapid algae monitoring.