Microcystis, the most frequently observed genus among cyanobacterial blooms, exhibits significant morphological diversity and pronounced spatio-tempo variation. However, the seasonal distribution patterns of its distinct morphological characteristics remain unclear. This study systematically analyzed the morphological features, spatio-temporal distribution patterns, and coupling relationships with environmental factors (temperature, nutrients, etc.) of Microcystis in Chaohu Lake from 2022 to 2024. Results indicate: Significant differences exist among Microcystis species in colony size and single-cell diameter. M. panniformis and M. aeruginosa exhibit the largest colony sizes, significantly exceeding those of M. flos-aquae and M. botrys. M. wesenbergii possesses the largest cell diameter, significantly exceeding M. botrys, M. aeruginosa, and M. viridis, while M. flos-aquae and M. ichthyoblabe exhibit the smallest diameters. These phenomenon exhibited distinct differences in response to nutrients (nitrogen, phosphorus) and temperature. Nitrogen and phosphorus were key nutrients influencing Microcystis population size and cell diameter, with significant differences in the distribution proportions of different species across total nitrogen and temperature ranges. During the cold season, M. viridis and M. pseudofilamentosa exhibited higher frequencies. As water temperatures rose 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 Microcystis cell diameter. Temperature and phosphorus show significant correlations (p<0.05) with cell diameter in most species. This study aims to provide scientific basis for understanding the ecological adaptation mechanisms of Microcystis in Chaohu Lake and for managing cyanobacteria in eutrophic lakes.