Phytoplankton is a major participant in the material and energy cycles of lake ecosystems, and obtaining information on its community structure is of great significance in coping with and regulating lake ecosystems. In this study, we examined the community characteristics of eukaryotic phytoplankton in the western half of Chaohu Lake in winter and summer by high-throughput sequencing. A total of 7 phyla and 71 Genus of eukaryotic phytoplankton were detected during the survey, 7 phyla and 59 Genus in summer and 5 phyla and 27 genera in winter, dominated by Chlorophyta and Bacillariophyta, and the dominant genus varied greatly in winter compared with those in summer. The mean values of Shannon-Wiener index in summer and winter were 1.83 and 1.88 respectively, and the mean values of Pielou index in summer and winter were 0.75 and 0.83 respectively. The mean values of both diversity indices were smaller in summer than in winter. The results of water quality analysis indicated that TN and TP were relatively high in the western half of Chaohu Lake during the study period, and the physicochemical of the water body were significantly different between summer and winter (p≤0.05). Redundancy analysis showed that PO4--P concentration, TN concentration, TP concentration and NH4+-N concentration had the greatest explanatory rate for the eukaryotic phytoplankton community, the effect of PO4--P concentration reaching a significant level (p≤0.05). Mantel correlation analysis showed that there was a good correlation between eukaryotic phytoplankton abundance with WT, DO, pH, NH4+-N, TN and Chl.a. Variance Partitioning Analysis showed that seasonal factors explained the eukaryotic phytoplankton community the most.