Microcystis, the most frequently observed genus in cyanobacterial blooms, exhibits significant morphological diversity and pronounced spatiotemporal variation. However, the seasonal distribution patterns of its distinct morphological characteristics remain unclear. This study systematically analyzed the morphological features, spatiotemporal distribution patterns, and coupling relationships with environmental factors (temperature, nutrients, etc.) of Microcystis in Lake Chaohu from 2022 to 2023. The results indicate that there are significant differences in colony size and cell diameter among Microcystis species. M. panniformis and M. aeruginosa have the largest colony sizes, which are significantly larger than those of M. flos-aquae and M. botrys. M. wesenbergii has the largest cell diameter, which is significantly larger than those of M. botrys, M. aeruginosa, and M. viridis, while M. flos-aquae and M. ichthyoblabe have the smallest diameters. This morphological differentiation was accompanied by differential responses to nutrients (nitrogen and phosphorus) and temperature. Nitrogen and phosphorus were the key nutrients affecting the colony size and cell diameter of Microcystis, with significant differences in occurrence frequency of different species across total phosphorus and temperature ranges. During the cold season, M. viridis and M. pseudofilamentosa had higher frequencies. As water temperatures increased into the warm season, the community shifted toward higher frequencies of M. wesenbergii, M. novacekii, and M. aeruginosa. In the hot season, M. botrys and M. smithii became the most frequent species. Correlation analysis and regression models further revealed the regulatory effects of environmental factors on the cell diameter of Microcystis. Temperature and phosphorus showed significant correlations with cell diameter in most species. This study aims to provide a scientific basis for understanding the ecological adaptation mechanisms of Microcystis in Lake Chaohu and for the management of cyanobacteria in eutrophic lakes.