We surveyed the spatial distribution characteristics of the phytoplankton community in the Yangtze River Estuary. A total of 157 species from 71 genera were identified and the average density were 3.31×10⁵ cells/L. Bacillariophyta was the dominant group, which was 61 species of 25 genera and its species number accounted for 39% of all species. Lyngbya limnetica, Oseillatoria agardhii, Oseillatoria amphibia, Oseillatoria tenuis, Chlorella vulgaris and Skeletonema costatum were the dominant species. Phytoplankton density ranged from 3.27×10⁴ to 1.50×10⁶ cells/L and there is no difference between the north branch, south branch and the main river. The homogeneity index between the north branch and the south branch varies little. The cell abundance and diversity index of the south branch are significantly higher than those of the north branch. The correlation analysis between phytoplankton and environmental factors showed that the species of phytoplankton and cell abundance were significantly positively correlated to temperature and chlorophyll a and were significantly negatively correlated to salinity. The diversity index and homogeneity index were significantly positively correlated to temperature and chlorophyll a and were significantly negatively correlated to conductivity. The cell abundance of Cyanophyta was significantly positively correlated to temperature and was significantly negatively correlated to dissolved oxygen and salinity. The cell abundance of bacillariophyta was significantly positively correlated to conductivity and was significantly negatively correlated to temperature. The environmental factors that have a significant impact on the distribution of phytoplankton species and density in the surveyed waters are salinity, conductivity, dissolved oxygen, temperature and chlorophyll a. Therefore, the environmental factors of the Yangtze River Estuary affect the spatial and temporal changes of phytoplankton community structure.