In order to explore the structure of zooplankton community in the National Aquatic Germplasm Reserve for Endemic Fish of Jinjiang River in different seasons, water samples were quarterly collected in January, April, July, and December, 2015. The analysis results showed that 82 species belonging to 51 genera and 4 phyla were sampled, among which the rotiferos, protozoa, copepod and cladocera accounted for 46.34%, 29.27%, 15.85% and 8.54%, respectively. 16 species of 6 genera and 4 phyla were identified as dominant species, including 6 species of rotiferos, 4 of protozoa, 4 of cladocera and 2 of copepod. The range of zooplankton density was 297.76~1430.10 ind/L and the average was 855.13ind/L. The range of zooplankton biomass was 5.73~26.36mg/L and the average was 14.37mg/L. Margalef index (Dm) ranged from 3.18~4.90 with the average being 3.96; Shannon-Weiner index (H') ranged from 2.11~3.12 and the average was 2.81; Peilou index (J') ranged from 0.81~0.89 and the average was 0.86. The study indicated that, under the common influence of both the degressive pressure from predators and the decrease in food organisms, small individuals like protozoa and rotifers could benefit from the external circumstances of the reserve, and as a result, ecological dominance of zooplankton community were inclined to these groups. Besides, impacted by hydrological characteristics, the number, density and biomass of zooplankton species as well as the biodiversity index of the core area of Jinjiang River excelled those of the experimental area in general.