Island and reef lagoon is an important environmental field for the evolution of island and reef biodiversity, and plays an important role in the material circulation and energy flow of island and reef water ecosystem. The ecological function of microzooplankton is one of the important research contents to analyze the composition, flow direction and energy flow efficiency of primary productivity of lagoon ecosystem in Nansha Islands waters. In this paper, microzooplankton and ecological environment were investigated in the surface waters of Zhubi Reef, Meiji Reef and Yongshu Reef lagoon, the key islands and reefs of Nansha Islands, and the community structure and its relationship with environmental factors were studied, and the grazing pressure of microzooplankton was studied by dilution culture experiment. There are 20 species of microzooplankton in the investigated waters, with the total abundance ranging from 320 to 1 460 ind/L, among which the abundance of Ciliated ciliate is the highest. The abundance of C. ciliate is highest in the western waters of Zhubi Reef lagoon (ZB-1), while the abundance of A. ciliate appears in the middle waters of Yongshu Reef lagoon (YS-3), and the maximum value of Nauplius larva appears in the northern waters of Meiji Reef lagoon (MJ-2). The cluster analysis shows that the community similarity of microzooplankton in the middle area of lagoon was relatively high, and dissolved oxygen is the most important factor affecting microzooplankton community structure in these islands and reefs, with its most obvious influence on MJ-3 station. The growth rate of phytoplankton in the lagoon waters of the three major islands and reefs was 0.22-1.36 d⁻¹. The grazing rate of microzooplankton ranged from 0.22 to 0.60 d⁻¹, and the micro-zooplankton consumed about 20.5%-45.1% of the existing phytoplankton every day, equivalent to 37.1%-222.9% of the primary productivity. This study shows that different environmental and biological factors on the three major islands and reefs of Nansha Islands have influenced the different grazing pressures of microzooplankton, thus forming different evolution mechanisms of microzooplankton biodiversity on each island and reef. This study provides data support for the energy flow of microbial loops in the lagoon ecosystem under the ecological effects of islands and reefs.