Abstract: In order to explore the eutrophication of Danjiangkou Reservoir and ensure the security of water quality in the middle line of the South-to-North Water Transfer Project, community structure of phytoplankton and 14 environmental variables in the reservoir bays were monitored seasonally in 2017. According to the monitored data, we analyzed the spatial and temporal distribution of phytoplankton and the main environmental factors influencing the distribution pattern with Pearson correlation analysis and Redundancy Analysis. 7 phylum and 57 genera phytoplankton were identified and the annual algae density ranged from 2.73×106 to 6.87×106 cells/L, with an average of 4.89×106 cells/L. The phytoplankton community was dominated by Bacillariophyta, Cyanophyta, and Chlorophyta. Diatoms and Cyanophyta dominated in spring. Chlorophyta, Cyanophyta and Cryptophyta dominated in summer. While Diatoms, Cryptophyta and Cyanophyta dominated in autumn and winter. The dominant species in four seasons were Aphanizomenon (Cyanophyceae) and Cryptophyceae. According to the indices of Shannon-Wiener, Margalef and Pielou, in summer, algae diversity was high, and Cyanophyta was dominated. In winter, algae diversity was relatively low, and there was no significant difference in population numbers. According to the comprehensive nutritional status index, the eutrophication degree of the bay was around intermediate nutrition and eutrophication level. Total nitrogen had impacts on the distribution of phytoplankton. Total nitrogen concentration ranged from 1.08 to 1.88 mg/L with an average of 1.47 mg/L. phosphorus concentration was the main factor influencing algae density in the Danjiangkou Reservoir bay. RDA analysis showed that the major environmental factors affecting phytoplankton community were water temperature, silica and conductivity.