Sampling surveys were conducted in April, July, October 2017 and January 2018 in two small lakes(Donghu Lake and Liuqiao Lake)of Huaibei excavating coal subsidence region to explore the seasonal variation of Rotifer community structure and its relationship with environmental factors. A total of 32 species belonging to 15 Genera and 13 families of rotifers were recorded in Donghu Lake, and 25 species belonging to 12 Genera and 10 families were recorded in Liuqiao Lake. The annual average density and biomass of rotifer in Donghu Lake(2 722 ind. /L and 3. 04 mg/L)were significantly higher than that in Liuqiao Lake(1311 ind. /L and 1. 30 mg/L). The dominant species in Donghu Lake are Trichocerca capucina, Trichocerca pusilla, Filinia longiseta, Polyarthra dolichoptera, Polyarthra vulgaris and Keratella cochlearis, whereas T. pusilla, P. dolichoptera, Cephalodella exigna, P. vulgaris, K. cochlearis and Filinia maio dominated in in Liuqiao Lake. The Lake Donghu and Lake Liuqiao were moderate eutrophication status. Water temperature, total nitrogen, total phosphorus and chlorophyll-a concentration are the important factors affecting the change of the community structure of rotifers in the two lakes. The predation pressure of Hypophthalmichthys molitrix and Aristichthys nobilis indirectly affected the community structure of rotifers in the two lakes.