Abstract: Based on the data collected from three oceanographic surveys in the east area of north (30.68°—30.83° N,121.67°—121.87° E), the east area of south (29.95°—30.24° N,121.60°—121.85° E), and the west area of north (30.58°—30.77° N,121.31°—121.56° E) Hangzhou Bay during the autumn of 2009, 2011 and 2012, we analyzed the species composition, ecological groups and the similarity of zooplankton community, as well as influencing factors. The results indicated that a total of 14 species belonging to 6 groups were identified in the west area of north Hangzhou Bay. Tortanus vermiculus was the predominant species. The zooplankton assembles were mainly influenced by the runoff strength of the Qiantang River. The zooplankton fauna was mainly composed of the subtropical estuarine brackishwater species, accounting for 79.8% in the total abundance. A total of 19 species belonging to 6 groups were identified in the east area of north Hangzhou Bay. The composition of zooplankton community was mainly influenced by the Changjiang diluted water and offshore water of the East China Sea. It was mainly composed of warmtemperature and subtropical nearshore lowsalinity species, accounting for 43.5% and 31.1% in the total abundance, respectively. In the east area of south Hangzhou Bay, a total of 25 species belonging to 7 groups were identified. The composition of zooplankton community was mainly influenced by the offshore water of the East China Sea. The dominate ecogroup types were subtropical nearshore lowsalinity and subtropical nearshore species, accounting for 72.3% and 18.3% in the total abundance, respectively. And the ecological groups of species with the highest abundance was Labidocera sinilobata, accounting for 65.3% in the total abundance. By hierarchical cluster analysis and nonmetric multidimensional scaling (NMDS) method, it was found that the zooplankton communities in the three parts of Hangzhou Bay were significantly different, which were closely associated with the impacts of different water masses from these parts.