In order to determine the influence of hydraulic regulation and environmental variables on rotifer community structure in pumped-storage reservoirs sharing the same water input but different hydraulic conditions, a through-flowing reservoir and an intermediate retention time reservoir were intensively sampled from August 2016 to July 2017. A total of 37 species of rotifers were identified. Common species in both reservoirs are from the genus Brachionus, Trichocerca, Keratella, Filinia and Polyarthra accounting for 58% and 64% of the total rotifer species in the through-flowing reservoir and the intermediate retention time reservoir, respectively. Although the species composition of the two reservoirs are quite similar, the dominant species were different. B. angularis, B. falcatus, B. forficula, B. diversicornis, P. euryptera, Synchaetidae stylata and Ploesoma truncatum dominated in the through-flowing reservoir; while Asplanchna brightwelli, B. diversicornis and B. falcatus dominated in the intermediate retention time reservoir. The Bray-Curtis dissimilarity of rotifer community structure for the two reservoirs is from 0.42 to 0.77. Redundancy analysis showed that chlorophyll-a and water temperature were the most important environmental variables explaining the variation of rotifer communities in the two reservoirs. The Bray-Curtis dissimilarity was significantly positively correlated with the environmental Euclidean distance based on chlorophyll-a concentration and water temperature (R_adj²=0.426, P<0.05). The results indicated that although they have the same water input, chlorophyll-a concentration and water temperature are significantly different due to the distinct hydraulic conditions of the two reservoirs resulting to differences in their rotifer community structure.