The Liuxihe Reservoir is a large canyon reservoir located on the Tropic of Cancer in Guangdong Province, and is used as a source of drinking water. The diversity and dynamics of rotifer species as an indicator group of water quality and ecosystem health, and environmental variables were investigated monthly in the pelagic zone of the reservoir from 2013 to 2014. We used the R language program (MASS, vegan, and packfor packages) to analyze the species diversity and community structure of rotifers in the pelagic zone of Liuxihe Reservoir. The rotifer community structure was analyzed using principal component analysis (PCA), redundancy analysis (RDA), nonmetric multidimensional scaling (NMDS), and variation partitioning. In the present study, Liuxihe Reservoir is an oligotrophic or mesotrophic water body, with annual averages of total phosphorus of 0.019 mg/L and water transparency of 2.55 m. Both total phosphorus and water transparency were slightly higher in the wet seasons from May to September than dry seasons (October to April). In total, 40 species were observed during the two-year investigation. The observed species richness ranged from 8 to 19 monthly, with a monthly average of 13. Keratella cochlearis, Polyarthra euryptera, Pompholyx sulcata, and Collotheca sp. were the dominant species. The average total abundance was 68.9 and 66.9 individuals/L in 2013 and 2014, respectively. The species richness was higher in wet than in dry seasons, whereas the Simpson index showed the opposite pattern. The average community distance, which was measured by the Bray-Curtis distance, was higher in dry than wet seasons, indicating that the rotifer community similarity was higher in wet than dry seasons. Water temperature and other variables of water quality were more stable in wet seasons. As a result, species dominance became stronger and rotifer communities were more similar. PCA indicated that Ascomorpha, Collotheca, Polyarthra, Trichocerca, Pompholyx, Asplanchna, and Ploesoma species showed significant temporal variation. This rotifer community structure is representative of tropical and subtropical China, where there is less water temperature fluctuation, allowing more species to occur throughout the year. Variation partitioning and RDA of the rotifer community with environment variables demonstrated that physical environment variables including temperature, dissolved oxygen, Secchi disk depth, precipitation, and water retention time explained the variance of the rotifer community, and among all the measured variables, water temperature and food availability were the two key factors explaining community structure variation, and precipitation was a macroscopic indirect factor affecting the variation of rotifer community. Most rotifer species are filters at low tropic levels in the pelagic zone of the Liuxihe Reservoir, with a small body size and short life span, and their communities responded to the variation of environmental factors similarly to phytoplankton communities.