Abstract: This study analyzed the distribution patterns and seasonal variation of zooplankton, and the effects of the water masses based on the data collected from four oceanographic surveys in the coastal waters of northern Fujian (120.10°E—120.65°E, 26.35°N—27.07°N) during the summer, autumn, winter and spring from 2015 to 2016, we analyzed the distribution patterns and seasonal variation of zooplankton, and the effects of the water masses. The results indicated that the average biomass of zooplankton was was followed as summer (479.51 mg/m³)>autumn (257.37 mg/m³)>spring (241.86 mg/m³)>winter (84.05 mg/m³), and the average abundance of zooplankton was was followed as summer (156.36 ind./m³)>spring (91.57 ind./m³)>autumn (40.34 ind./m³)>winter (21.82 ind./m³). The average biomass and the abundance of zooplankton both decreased from summer, autumn to winter in turn, while increased in spring. The average biomass in autumn was higher than that in the spring, on the contrary, the average abundance was lower than that in the spring. In summer, winter and spring, the distribution of total biomass and total abundance of zooplankton were generally consistent. While in autumn, the distribution patterns were almost in the opposite direction. Sagitta bedoti and Canthocalanus pauper were the most important species which had impact onregulating the distribution of total abundance in summer, and Desmophyes annectens was the most important species for the distribution of total abundance in autumn. In winter, Acrocalanus gibber, Eucalanus subcrassus and Sagitta bedoti had an important impact onmainly mediated the distribution of total abundance. Muggiaea atlantica and Canthocalanus pauper were the two species that had a higher proportion of total abundance in spring. The seasonal variation of the Taiwan warm current and Zhe-Min coastal current was the root factor that decidedto decide the distribution patterns of zooplankton in each season. The results not only had an important theoretical significance for understanding and evaluating the dynamics of regional marine ecosystem and biodiversity changes, but also could improved the relationship between the ecological characteristics of zooplankton and water mass changes in China’s offshore waters.