Effect of environmental factors on the seasonal variations of zooplankton communities was investigated in the semi-closed Yeoja Bay, Korea from February, April to August, and November 2021. Out of a total 49 species of zooplankton were collected with a predominant of neritic copepods (mainly Paracalanus orientalis, Acartia omorii, Acartia ohtsukai, Centropages abdominalis, Ditrichocorycaeus affinis, and Oithona sp.), accounting for 58.9% of the total abundance of zooplankton. The diversity indices indicated a relatively highest in July, suggesting that diversity is influenced by seasonal temperature, N. scintillans, and neritic copepods species. A cluster analysis with non-metric multidimensional scaling revealed four groups of zooplankton communities. The February sample clustered into Group A, having the lowest mean total abundance and species diversity of zooplankton, consisting mainly of N. scintillans located the whole region. Cluster Group B from the spring season (April to May) and contained the species diversity with some neritic copepods. Cluster Group C from the summer season (June to August) mainly comprised P. orientalis, A. ohtsukai, Oithona sp., and hydromedusae. Cluster Group D from the autumn season (November) mainly comprised P. orientalis, Temora discaudata. Redundancy analysis indicated that abundance is positively correlated with temperature, salinity, and pico chlorophyll-a concentrations. This study showed that planktonic larvae (such as branchyura larvae) and some copepods (including A. omorii, A. ohtsukai, C. sinicus, and C. abdominalis) were significantly vulnerable to zooplankton community of temperature, salinity, and pico chlorophyll-a concentrations.