The pistol shrimp generates shock waves, which is resulted from the generation and collapse of cavitation bubbles when the claws open and close, powerful enough to stun large fish. Microcystis aeruginosa, a cyanobacteria that is the main cause of algal blooms, has the gas-vacuole inside the cell. If the shock wave can be generated by inducing the collapse of the gas-vacuole inside the cell, Microcystis can be destroyed in the short-term or disrupted due to damage to the internal system in the long-term. In this paper, we experimentally studied the disruption characteristics of Microcystis by mimicking the shock wave generating from collapse of cavitation of pistol shrimp. In order to mimic the characteristic of pistol shrimp and analyze their effects for the gas-vacuole, ultrasonic individually with different frequency was used to induce cavitation and collapse of bubbles. Due to the nature of Microcystis cell, the disruption rate for each frequency was observed through short-term and long-term follow-up. The experimental results were compared by various methods of microscope, chlorophyll content, and cell counting. It was shown that there exist specific frequencies that keeping or increase the disruption rate in the long-term.