In order to characterize the species composition, abundance, biomass and community structure of zooplankton in Qiongzhou Strait and their influencing environmental factors, field samplings were conducted with vertical net in June (rainy season) and November (dry season), 2022. A total of 62 species of zooplankton were identified, including 34 species of arthropods, 14 species of Cnidaria, 9 species of larvae, 3 species of Chaetognatha, 1 species of Chordata and 1 species of Mollusca. The dominant species in rainy season were Subeucalanus subcrassus, Euchaeta plana and Canthocalanus pauper. The dominant species in dry season were Subeucalanus subcrassus, Flaccisagitta enflata and Canthocalanus pauper. The average values of abundance and biomass of zooplankton in the rainy season were 66.32 ind./m³ and 359.9 mg/m³, and those in the dry season were 93.0 ind./m³ and 163.4 mg/m³, respectively. The average diversity index (H′) was 2.20, the average evenness index (J′) was 0.79, and the average richness index (d) was 5.41. The average diversity index (H′), evenness index (J′) and richness index (d) of the dry season were 2.33, 0.81 and 6.75, respectively. The community structure of zooplankton was mainly correlated with nutrients, suspended solids and water temperature. Overall, the zooplankton community structure in Qiongzhou Strait was greatly influenced by water temperature, water flow velocity and terrestrial inputs from rivers.