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Large-scale macro-algal blooms of Ulva prolifera (also called green tides) have appeared each summer since 2008 in the western Yellow Sea. In this study, we investigated the temporal variability in zooplankton community in the western Yellow Sea and its possible links to green tides using data from a long-term plankton survey off the coast of Qingdao, China. Environmental conditions observed in the study area during the green tide period (GTP: June-August, 2008-2013) were compared to the non-green tide period (NGTP: June-August, 2005-2007), to support the contention that variations observed in zooplankton community may be attributed to the green tides, as opposed to natural climatic or environmental variations. Zooplankton assemblage structure observed during the GTP was then compared to the NGTP. Significant variations were detected both in zooplankton abundance and assemblage structure between the two defined periods. The abundance of zooplankton, mainly copepods, was significantly decreased during the GTP. Meanwhile, the relative abundance of copepods decreased by approximately 10% and that of gelatinous zooplankton, including appendicularians, chaetognaths, and medusae, almost doubled (ca. increased by 6.4%). The dominant species of meroplankton completely changed, specifically, polychaeta, and echinoderm larvae were more dominant than decapod and bivalve larvae. With regard to zooplankton size structure, the NGTP showed a higher size diversity with more small-sized organisms, while the GTP showed a lower size diversity in the community. According to general linear models, the interannual variation in summer zooplankton abundance was significantly correlated with green tides. These results indicate that the temporal changes in zooplankton community may have a close link to the green tides.