Based on the water quality and biological monitoring data of the Yangtze River Estuary in the summer from 2009-2021, the dominance index, Shannon-Wiener diversity index, Margalef richness index, Pielou evenness index, and the redundancy analysis were used to analyze the characteristics and influence factors of plankton community structure by partition. Results showed that, (1) The number and density of phytoplankton showed an upward trend. The community structure was dominated by diatoms, while the proportion of methanogens increased in recent years. The number, density and biomass of zooplankton showed an overall decreasing trend, and the community composition was dominated by copepods. The number of phytoplankton and zooplankton species showed an increasing trend of from the nearshore to the offshore. (2) The diversity of zooplankton is better than that of phytoplankton, and the spatial distribution of the two biodiversity is more consistent. The diversity and richness of plankton in the area with salinity >25‰ were both relatively high, while the species are few but evenly distributed in the area with salinity <5‰. The range of salinity from 5‰ to 25‰ had more zooplankton species but with uneven distribution. (3) The results of redundancy analysis showed that water temperature, salinity, light, and nutrients were the main influencing factors of the plankton. In addition, predation among organisms also had an important effect. The results can provide a basis for the environmental management of the Yangtze River Estuary.