Abstract: Zooplankton community characteristics are related to potential fishery resources and effected by environmental factors in coastal reefs. According to four seasonal cruises on fishery ecology in artificial reefs and island reefs of Daya Bay (114.540°E−114.669°E, 22.540°N−22.639°N) in 2015, we analyzed the zooplankton community characteristics and impacts of environmental factors on ichthyoplankton. Altogether 130 zooplankton species were identified. The community structure of zooplankton experienced seasonal variation, including spring group, summer group, autumn group and winter group. The distinct dominant species were Penilia avirostris and Noctiluca scintillens in spring and summer, and Acartia erythraea and Flaccisagitta enflata in autumn and early winter. The annual means of Margalef index, diversity threshold levels, abundance and biomass were similar and the seasonal variance of zooplankton quantity was significant between the two fish reefs. The abundance of larvae was effected by Copepods and the distribution of fish spawns was decided by hydrologic conditions. The spatio-temporal variation of zooplankton community characteristics, such as biodiversity indices, community structure, abundance and distribution, were response to temperature, salinity and zooplankton distribution caused by seasonal variation of water mass.