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• Inter-annual and seasonal variations in zooplankton community structure were analyzed. • Warmer conditions in spring of 2017–2018 benefited copepod community. • A regime shift might have occurred in 2016/2017 in the Yellow Sea. Inter-annual and seasonal variations in zooplankton community structure in the Yellow Sea, China were studied in relation to climatic events and local environment from 2014 to 2018. Three zooplankton assemblages were identified based on cluster analysis, which were associated with seasonal temperature changes. Group 1 composed spring stations with moderate water column temperatures. The spring zooplankton assemblage had the highest mean total abundance with crustaceans, including euphausiids, amphipods and copepods dominating samples. Stations in the basin area during summer–autumn and all stations in winter composed Group 2, with low bottom water temperatures being a prominent feature. Zooplankton assemblage of Group 2 mainly consisted of a mixture of low-temperature species and some tropical species that were transported into the region by the Yellow Sea Warm Current. Coastal stations with high water temperature during summer–autumn made up Group 3. Zooplankton was characterized as summer–autumn neritic assemblage with high jellyfish abundance. Some meroplankton and brackish water species, i.e. Labidocera euchaeta , were indicator species confirming the influence of the river discharge. Both PDO (from positive to negative) and ENSO (from negative to positive) reversed their signs in 2016/2017. The abundances of total zooplankton, Noctiluca scintillans , Calanus sinicus and small copepods were much higher in spring of 2017–2018 compared to spring 2015 due to the warmer conditions. In addition, zooplankton community of summer 2017 was characterized by high abundances of copepods and gelatinous zooplankton, Diphyes chamissonis and Doliolum denticulatum. This was influenced by a strong river runoff and warm current transport, and differed from 2014 and 2016 summers. Our results suggest that a regime shift occurred in 2016/2017, which was supported by sharp changes in physical settings as well as zooplankton community structure in the Yellow Sea. However, a longer time series is required to uncover detailed processes and response mechanisms of environmental conditions of the Yellow Sea to climate change. [ABSTRACT FROM AUTHOR]