Zooplankton is an important component of the coral reef ecosystem, but studies on this component are insufficient in China. Based on 13 samples collected in July 2012, the characteristics of zooplankton community in the Meiji coral reef waters were studied. It was found that the reef waters are rich in zooplankton species and a total number of 138 species belonging to 15 taxa was recorded. The dominant species were fish eggs, Oikopleura longicauda, Macrura larvae, Centropages orsinii, Oikopleura sp., Sagitta robusta, Brachyura zoea, and Fritillaria haplostoma. According to habitats of the species, they could be categorized into warm-water coastal fauna and warm-water oceanic fauna. There was no obvious species dominating throughout three types of habitats in the reef waters and the species compositions and dominant species varied with habitats. The dominant species compositions in seaward slope were the most complex and 15 species were recorded. The main dominant species were Oithona plumifera, Thalia democratica and Oikopleura sp. in seaward slope. The similarities of species compositions of seaward slope to lagoon and to reef flat were only 27.8% and 21%, respectively, whereas, the similarity of species compositions between lagoon and reef flat was as high as 77.8%. The reef waters are rich in zooplankton diversities. The average indexes of species richness, diversity and evenness were 4.93, 3.33 and 0.67, respectively, and the overall threshold value of diversity was 2.43. The threshold values of seaward slope, lagoon and reef flat were 4.04, 1.98 and 1.38, respectively, showing that the zooplankton diversity was the highest in the seaward slope waters. The mean abundance and wet biomass of zooplankton were 117.70 ind/m³ and 69.01 mg/m³, respectively, and the zooplankton abundance was mainly composed of larvae. The abundance of larvae was 52.32 ind/m³, taking up 44.5% of total zooplankton abundance. The zooplankton community in the reef waters could be classified into the lagoon-reef flat group and the seaward slope group. The test of One-way ANOSIM showed that compositions of the two groups were significantly different (R= 0.865, P= 0.001). Due to topographical heterogeneity and differences in hydrodynamic conditions in the reef waters, the regional variation of the zooplankton community was obvious. Being the low wave energy zone, the hydrodynamic changes, winds and waves of the lagoon is the least. In the lagoon waters, the zooplankton diversity was higher, but the biomass was the lowest. Whereas in reef flat, due to medium wave energy and moderate hydrodynamic changes, the zooplankton abundance and biomass was higher, with uneven distributions, and the diversity was lower. Adjoining the open ocean, seaward slope is steep in topography, drastic change in water depth, and upwelling can occur there. The diversified environment conditions are fit for the growth of a variety of zooplankton species. Therefore, the species richness and diversity of zooplankton in the seaward slope was the highest. However, located in the high wave energy zone, the hydrodynamic and water turbulence in the seaward slope are the strongest. The conditions do not favor zooplankton growth and the zooplankton abundance there was the lowest.