To understand the community structure of zooplankton offshore of northwest Hainan Island and explore the relevant environmental factors affecting their distribution, we conducted seasonal investigations in sites offshore of northwest Hainan Island in November 2016 and February, May, and August 2017. A redundancy analysis model was used to analyze the relationship between the community structure and environmental factors. Nonmetric multidimensional scaling ordination analysis was applied to test the differences between the communities. Furthermore, ANOSIM similarity testing was used to analyze the differences among the communities. A total of 215 species, belonging to 113 genus and 7 phyla, were identified, among which 134 species were present in autumn and 94 in summer. The number of identified species was relatively close between winter (113 species) and spring (111 species). The seasonal differences in the average abundance of zooplankton was significant, being highest in winter (152.43 ind/m³) and lowest in spring (64.76 ind/m³). The seasonal differences in the average biomass of zooplankton was also significant, being highest in winter (263.68 mg/m³) and lowest in spring (59.13 mg/m³). The RDA showed that the water depth, phytoplankton abundance, transparency, surface temperature, surface dissolved oxygen, and surface total nitrogen have significant correlations with the community structure of zooplankton. Among these environmental factors, the water depth was the key factor, which affected the variation in the zooplankton community structure according to the seasons. Tropical warm water species were the dominant groups in spring and summer, while offshore warm water species were dominant in autumn and winter, suggesting an ecological differentiation among ecological groups. This was mainly caused by the flow direction of the current in Beibu Bay. Compared with the same latitude (waters of Cheng Mai and Dongzhai Harbor) and a lower latitude (Sanya Bay and waters of Wanning), higher amounts of zooplankton species were found offshore of northwest Hainan Island. When compared with Beibu Bay and the coastal waters of the northern South China Sea, the number of zooplankton species in this study was lower. However, the changing tendencies of dominant groups, ecological communities, and seasonal variation characteristics were consistent among these areas.