Abstract: In order to investigate the characteristics of plankton community structure and its influencing factors in the waters of the Yangtze River Estuary during summer time. Based on the water quality and biological monitoring data of the Yangtze River Estuary in the summer of 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. The results showed that: (1) The number and density of phytoplankton showed an upward trend. The community structure was dominated by Bacillariophyta, and the proportion of Dinophyta increased in recent years. The number, density and biomass of zooplankton showed an overall downward 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 was better than that of phytoplankton, and the spatial distribution of the two biodiversity was more consistent. The diversity and richness of plankton in the area with salinity >25‰ were both relatively high, while the area with salinity <5‰ had fewer species, but they were evenly distributed. There were more zooplankton species in the salinity rang of 5‰ to 25‰, the distribution was uneven. (3) The redundancy analysis results showed that water temperature, salinity, light, and nutrients were the main factors affecting the plankton. In addition, predation among organisms also had an important effect. The study shows that the spatial and temporal distribution of plankton community structure in the Yangtze River Estuary in summer is more obvious. In the entrance area and some estuary areas, the input of land sources brought abundant nitrogen and phosphorus nutrients, and the mixing of salty and fresh water in the estuary area promoted the growth of plankton. The seawater area was affected by the Kuroshio tide, which had high salinity and rich nutrient salt content. The Kuroshio tide carried a large number of plankton into the sea area, improving the richness and diversity of plankton.