The Zhenjiang Yangtze Dolphin Nature Reserve in Jiangsu Province is the one of the primary habitats of the Yangtze finless porpoise habitat in the lower reaches of the Yangtze River. In order to understand the community characteristics of zooplankton (including protozoa, rotifer, cladocerans and copepods), a filed investigation of zooplankton was conducted in the Zhenjiang Yangtze Dolphin Nature Reserve from January 2016 to October 2018. The temporal and spatial variations in zooplankton community structure and their relationship with environmental factors were analyzed. A total of 4 phyla, 41 genera, and 90 species of zooplankton were identified, which dominated mostly by protozoa (40 species), while rotifer, cladocerans and copepods were rather rare. A total of 8 dominant species were identified in all years, the zooplankton community in Zhenjiang nature reserve is generally miniaturized and dominated by protozoa (7 species) that feed on phytoplankton. The zooplankton density and biomass have significantly seasonal difference (P<0.05), and the temporal variability showed a trend that highest in summer and autumn, lowest in spring and winter. Pearson correlation and RDA analysis showed that water temperature, dissolved oxygen, pH and total Nitrogen were main factors related to significant differences in zooplankton communities among seasons. The variations of zooplankton community characteristics and fish potential production estimation through zooplankton indicated that, the aquatic ecology environment of nature reserve has improved when compared with historic data, but the situation of lack of fishery resources has not been changed yet, and nutrition requirements for porpoise were not optimistic. The results of this study can provide a theoretical basis for ecology monitoring and protective research of porpoise habitat in Zhenjiang Nature Reserve.