Abstract: In order to understand the current status of phytoplankton communities and their correlations with environmental factors at critical periods of fish life history in the mainstream of the Three Gorges Reservoir, phytoplankton communities and water environmental factors in 11 sampling sites belong to 4 sections in the mainstream of the Three Gorges Reservoir were investigated in the breeding period, fattening period and overwintering period of 2019. A total of 182 species of phytoplankton, belonging to 7 phyla, were collected, of which the community is mainly composed of Bacillariophyta, Chlorophyta and Cyanophyta. Phytoplankton species number and abundance were highest in the fattening period, less higher in the breeding period, and were lowest in the overwintering period. Spatially, the value presented a decreasing trend from the upper to the lower reservoir. Bacillariophyta and Cyanophyta dominated in the breeding period and the fattening period, with Bacillariophyta and Cryptophyta dominating in the overwintering period. The Shannon-Wiener diversity index, Margalef richness index, and Pielou evenness index were dramatically lower in the overwintering period than in the breeding period and the fattening period, and decreased from the upper to the lower reservoir in the fattening period. Spearman correlation analysis indicated a significant positive correlation between Bacillariophyta abundance and total phosphorus and suspended matter concentration, and between Cyanophyta abundance and water temperature, total phosphorus concentration. The results of Spearman correlation analysis also showed that the diversity of phytoplankton community was regulated by numerous environmental factors. Redundancy analysis (RDA) results further revealed that water temperature, total phosphorus, pH and suspended matter were the key factors regulating the community structure of phytoplankton in the mainstream of the Three Gorges Reservoir. Moreover, the phytoplankton community in the breeding period was mainly affected by nitrate-nitrogen, with water temperature, total phosphorus and suspended matter the main factors determining the phytoplankton community in the fattening period, and ammonia, pH and dissolved oxygen the main factors shaping the phytoplankton structure in the overwintering period. The results of this study could provide a certain scientific basis for protection and remediation of fishery ecological environment in the Three Gorges Reservoir.