In this study, we analyzed the species composition, ecological distribution, and spatial, diurnal, and interannual variation of zooplankton in the Yangtze River Estuary in the summers of 2017-2018. We used a 24 time-series analysis, a section stations survey, and the canonical correspondence analysis (CCA) to reveal the relationship between the abundance of dominant groups and the environmental variables. The results showed that there were 49 and 50 zooplankton species in the summers of 2017 and 2018, respectively, of which, Sagitta enflata, and were the dominant species. The SIMPER analysis indicated that the main contributors to the interannual variation of the zooplankton community were , and Thaliacea. CCA analysis showed that the surface temperature, bottom salinity, and surface chlorophyll a were the main environmental factors affecting the interannual variation of zooplankton groups, explaining 47.51% of the two-year zooplankton variation. Based on the spatial distribution of chlorophyll a in 2018, the stations were divided into chlorophyll a frontal and non-frontal area, which contained the L1-L2 and L3-L4 stations, respectively. The main contributors to the spatial differences of the zooplankton community were Euchaeta concinna. CCA analysis showed that the bottom salinity, bottom temperature, and surface chlorophyll a were the main environmental factors affecting the spatial variation of zooplankton groups, accounting for 56.31% of the variation in the composition of zooplankton in 2018. The results indicated that the different runoffs of the Yangtze river, diluting the water and causing changes in salinity and chlorophyll a, had an important impact on the interannual variation of the zooplankton community.