Similarity analyses were performed on zooplankton communities in the South Branch (SB), North Branch (NB), North Channel (NC), and offshore area (OS) of the Yangtze River estuary based on the survey conducted during spring and autumn from 2009 to 2010. According to the results of the hierarchical cluster analysis and non-metric multidimensional scaling. The zooplankton species occurring in this estuary in spring can be divided into two communities:I and Ⅱ.. Community I in OS is significantly different from community Ⅱ. Community I was dominated by offshore zooplankton species, e.g., Calanus sinicus (density of 35.30 ind/m³), which may be due to the effect of water masses. Few estuarine and coastal species were also observed during this period. As a result of the Yangtze River runoff, community Ⅱ was dominated by estuarine species; this community can be further divided into community Ⅱ-1 (NC), Ⅱ-2 (NB), and Ⅱ-3 (SB). Sinocalanus sinensis was the most dominant species across these subcommunities, present at varying densities. The differences in estuarine communities were mainly caused by the adaption of S. sinensis to freshwater environment. In autumn, the communities of the Yangtze River could be distinctly divided into four clusters:Ⅲ, Ⅳ, Ⅴ, and Ⅵ. Owing to the stronger runoff and the offshore water mass, there were considerable differences from the dominant species which led to form the different communities. Estuarine species prevailed in community Ⅲ (NC), with Tortanus vermiculus observed as the dominant species (3.08 ind/m³). Due to the small impact of the Yangtze River Runoff and with a high salinity in the waters of NB, community Ⅳ was mainly composed of coastal species. Furthermore, owing to the effects of offshoe currents and water mass, community Ⅴ (OS) was dominated by offshore species such as Calanus sinicus and marine species such as Subeucalanus subcrassus and Sagitta enflata. As a result of the stronger runoff of the Changjiang River, freshwater species dominate community Ⅵ (SB). Sinocalanus dorrii was the key species of community Ⅵ, with a high dominance(0.93). Thus, salinity and water masses were considered key factors to cause differences in zooplankton communities in the Yangtze River Estuary, and the differences between the offshore area and the estuarine areas were larger than those in the estuarine areas.