Coastal waters are ecosystems of great human and ecological interest, where complex processes occur. The interaction of physical (e.g., coastal currents, upwelling, tides, and advection), chemical (variable chemical properties including nutrient inputs), and ecological (e.g., biological production and its dynamics, and prey/predator interactions) processes induce high spatial and temporal variability in the water. This variability determines the abundance and structure of different biological communities present in coastal waters, in particular zooplankton, which are at the lower levels of the oceanic food chain. To understand coastal zooplankton community structure and explore its relationship with various environmental factors, a zooplankton survey was conducted in Sishili Bay. Fifteen sampling stations were chosen to study water temperature, salinity, transparency, DO, COD, inorganic nitrogen, phosphorus, silicate, and Chl a from March 2009 to December 2010. Sampling and testing methods followed those of the Specifications for Oceanographic Surveys and Specifications for Marine Monitoring. The relationships between zooplankton communities and various environmental factors were conducted by Pearson correlation analysis and canonical correspondence analysis (CCA). A total of 64 zooplankton species, belonging to 8 taxonomic groups, were recorded in Sishili Bay over the study period. Copepods and zooplankton larvae were the main taxonomic groups, accounting for 34% and 28% of total species, respectively, followed by Hydromedusa, accounting for 20%. Only one species each of Ctenophora and Chaetognatha were identified. The dominant species, which exhibited significant seasonal variability (P < 0.05), were Calanus sinicus (Y=0.183), Centropages abdominalis (Y=0.078), Sagitta crassa (Y=0.078), and Acartia hongi (Y=0.026). The ecological type of zooplankton in Sishili Bay was primarily temperate coastal and wide spread species. Four zooplankton community structure types were observed from the cluster dendrogram. Similar seasonal variations in the zooplankton community were observed in 2009 and 2010. The zooplankton community had high stability and reproducibility and similarity in different months of the same season reached more than 55%. The median total zooplankton abundance in Sishili Bay from 2009 to 2010 ranged from 40.5 individuals/m³ to 546.3 individuals/m³, with highest median abundances observed in May. The highest median values of zooplankton species and for the diversity index were recorded in August. The zooplankton biomass exhibited a significant seasonal difference (P < 0.05). The zooplankton biomass revealed an obvious bimodal annual variation trend and reached a maxima peak in May and a minor peak in October, with median biomass of 870.4 mg/m³ and 362.0 mg/m³, respectively. The stations with high zooplankton species were mainly distributed in the northern area of Yangma Island, whereas the inshore area, especially the Xinan River mouth, exhibited the highest zooplankton biomass. In present study, water temperature, COD, and silicates revealed a significant positive relationship with zooplankton species and the diversity index, whereas salinity, DO, and inorganic nitrogen exhibited a significant negative relationship with them. Canonical correspondence analysis (CCA) indicated that water temperature and salinity accounted for most of the zooplankton species variation, followed by silicates, Chl a, and COD, whereas phosphorus, DO, transparency, and inorganic nitrogen exhibited a weak influence on zooplankton community distribution.