Pressure treatment of Microcystis prior to discharge into the aquatic environment has been an emerging approach to relieve the Microcystis blooms. However, current literature has not noticed the changes of pressurized Microcystis on microbial community characteristics in water. We have evaluated the performance of variable pressure treatment protocols, and the most suitable case was proven as follows: pressuring Microcystis up to 0.7 MPa in 5 s at a pressure-accelerating speed of 0.14 MPa/s, and treating for 30 s. After treatment, the gas vesicles were efficiently destroyed and extracellular polymeric substance (EPS) on cells was exfoliated. The exfoliated EPS significantly affected phyla including Verrucomicrobiota associated with the degradation of organic matters, and thus affected community function, the energy metabolism was enhanced and uptake of dissolved organic phosphorus (DOP) by microorganisms increased after pressure treatment. This study was of significance for exploring the effects of pressurized Microcystis control measures on lake ecological environment.