Zooplankton is an important component of the aquatic ecosystem. Analyzing the community structure of zooplankton can provide a reference basis for water environmental protection. In March, June, September and December 2023, sampling surveys were conducted respectively in the Qixi reservoir and five streams of Qianjiangyuan National Park. During the investigation, a total of 127 species belonging to 70 genera of zooplankton were identified, including 55 species of rotifers, 28 species of protozoa, 24 species of cladocerans and 20 species of copepods. From spring to winter, the number of zooplankton species gradually increased. The average annual zooplankton density and biomass were 9.01 ind·L−1 and 20.8 μg·L−1 respectively in Qianjiangyuan National Park. The zooplankton density (23.1 ind·L−1) and biomass (56.5 μg·L−1) in autumn were both the highest values of the four seasons. In Qixi reservoir, the most dominant zooplankton species was Synchaeta sp. in spring and winter, and Nauplius in summer and autumn. In streams, the most dominant zooplankton species was Copepodite in spring, Centropyxis discoides in summer, and Centropyxis ecornis in autumn and winter. The results of Canonical correspondence analysis showed that temperature, dissolved oxygen, BOD5, pH and chlorophyll a were the dominant factors affecting zooplankton community.