To reveal the seasonal variations of zooplankton community and their drivers in reservoirs of the Chaobai River basin, 12 reservoir monitoring stations were deployed in September (autumn) and December (winter) of 2020, and March (spring) and June (summer) of 2021, respectively. Totally 90 zooplankton species belonging to 67 genera were identified in the four seasons, with the highest richness in summer and the lowest in spring. The mean abundance (231.5 ind./L) and biomass (0.199 mg/L) of zooplankton peaked in summer, while they were merely 60.8 ind./L and 0.075 mg/L in spring, respectively. Significant seasonal differences were observed in the structure of zooplankton community. Rotifers contributed the largest proportion of richness and abundance in autumn and summer, but the zooplankton in winter and spring were mainly dominated by protozoa. Strobilidium sp. was the most abundant species occurred in the four seasons of the reservoirs. Correlation analysis showed that the Shannon-Wiener diversity index of zooplankton was positively related with nitrite nitrogen and total organic carbon, while the richness was strongly associated with nitrate nitrogen, total nitrogen and total phosphorus. Canonical correspondence analysis exhibited that dissolved oxygen, water temperature, nitrite nitrogen, total organic carbon and conductivity were crucial in driving the seasonal distribution of zooplankton community. This study further provided supplementary data for the assessment of ecosystem health in reservoirs of the Chaobai River basin.