The seasonal variations of zooplankton community structure and species composition were studied based on the samples collected from four research cruises in China seas from July 2006 to December 2007. The results showed that a total of 1330 species of zooplankton belonging to 19 groups in 7 phyla, together with 47 types of pelagic larvae were identified in the China seas. The 7 phyla included Cnidaria, Ctenophora, Annelida, Mollusca, Arthropoda, Chaetognatha and Urochordata. The most dominant group of zooplankton is Arthropoda, including 782 species and accounting for 58.80%. Cnidaria ranks second with a total of 324 species, accounting for 24.36% of total species. Copepods and Medusae were the most dominant groups in numbers of species and abundance in the community structure of zooplankton in China seas. There was considerable seasonal variation in the community structure of zooplankton in China seas. There were more zooplankton species in summer and autumn than in spring and winter in the Bohai Sea and the Yellow Sea, and more zooplankton species in summer and spring than in autumn and winter in the East China Sea and the South China Sea. There were seasonal changes in numbers of pelagic larvae in China seas, with the highest number in autumn, followed by summer, spring and winter. The zooplankton communities in China seas might be divided into 6 ecological groups, which were coastal brackish water group, hypothermal hypersaline group, hyperthermal hypersaline group, hypothermal euryhaline group, hyperthermal euryhaline group and eurythermal euryhaline group, respectively. The correlation between community structure of zooplankton and main environmental factors were analyzed. Statistic analysis showed that there were significant correlations between zooplankton community structure and environmental factors such as temperature, salinity, water depth, dissolved oxygen, nitrate and pH. The most important environmental factors that influenced the changes of zooplankton community structure in China seas were water temperature and salinity.