Three small lakes at PXPJ site, PXGQ site and PXXQ site in the Huainan Panxie coal mine subsidence areas were chosen as research sites, which were characterized by different conditions in hydrology, ecological and environmental factors. The investigation of rotifer communities and aquatic environmental factors were conducted in the four seasons of 20132014 to address their relationship. A total of 32 species have been recorded, which belong to 15 genera. 25 species of the 13 genera at PXPJ site, 24 species of the 13 genera at PXGQ site, and 20 species of the 11genera at PXXQ site have been indentified. Keratella valga, Trichocerca rousseleti, Asplanchna priodonta, Asplanchna brightwelli, Polyarthra trigla Ehrenberg, Gosse were the dominate species in the lakes. Rotifer abundance were 500-2800ind./L at PXPJ site, 950-3350ind./L at PXGQ site, and 400-3900ind./L at PXXQ site. The average Shannon-Wiener diversity indexes for rotifer communities within the three studied sites were 2.71, 2.68 and 2.54 respectively, indicating β-type of medium pollution water quality in the aquatic zones.Redundancy analysis based on rotifer community and aquatic environmental factors showed that water temperature, conductivity and nutrient in the lakes are the main factors affecting the rotifer communities in those lakes.