Abstract: To study the community structure of phytoplankton in different aquatic bodies polluted by heavy metals and its relationships with environmental factors, field surveys were conducted in Youxian County and Wanshan District in November 2019. A total of 67 phytoplankton species were identified, belonging to 7 phyla and 52 genera. The community structure of phytoplankton has no remarkable difference between different water types (R=–0.022, P=0.549), but the two study areas were different (R=0.152, P=0.083). The communities were dominated by Chlorophyta, Bacillariophyta, and Cyanophyta. The phytoplankton abundance ranged from 1.11×10⁴ to 1.17×10⁷. The species richness of the phytoplankton community was 10—31 in Youxian County and 6—18 in Wanshan District, the Shannon-Wiener index of the phytoplankton community was 2.28—3.29 in Youxian County and 0.482—2.401 in Wanshan District, the evenness index of the phytoplankton community was 0.979—0.996 in Youxian County and 0.244—0.742 in Wanshan District. These three indices showed significant differences in different districts (P<0.05). Pearson correlation analysis indicated that COD_Mn, TOC and ORP were significantly positively correlated with phytoplankton abundance, and Cr, Se, Ba and V were significantly negatively correlated with phytoplankton abundance. Mantel test analysis indicated that COD_Mn, WT, pH, TC, IC, \rmPO_4^3 - -P and Co, Ni, Zn, Cd, and Pb were the key factors that explain the phytoplankton community structure. The canonical correlation analysis indicated that the changes in the phytoplankton community were more related to routine physics and chemistry index than to heavy metals. There were significant differences in phytoplankton community structure in heavy metal polluted areas, and heavy metal ion content and routine physics and chemistry index had significant influences on the community structure. These results provide a research basis for isolating heavy metal tolerant algal strains and carrying out subsequent transformation. Meanwhile, the research is of great significance to the management and protection of water ecosystem.