The spatial-temporal changes in rotifer species composition and community structure and their relationship with key environmental factors were investigated seasonally from May 2010 (spring) to February 2011 (winter) in a shallow freshwater lake, Lake Hongze, China. Totally 34 species of rotifer, belonging to 17 genera, were identified during the seasonal sampling. Keratella cochlearis, Asplanchna priodonta, Polyarthra dolichoptera, Brachionus calyciflorus and Keratella valga were the dominant species. Lake Hongze has three main areas that are Chengzihu, southwest and east area. The rotifer distribution in the three main areas was significantly different. There were 27, 26 and 19 species in Chengzihu, southwest, east area, respectively. Meanwhile, the maximum density and biomass of rotifers was found in the southwest area of Lake Hongze while the minimum was found in the east area. In terms of seasonal variation, the density and biomass of rotifer was highest in spring, with higher values in autumn. The density and biomass in summer was lowest in the four seasons. Their relationship with environmental factors was analyzed using canonical correspondence analysis (CCA). From the result of CCA, environmental factors such as water temperature, dissolved oxygen and chlorophyll-a that representing seasonal variations of water quality were significantly correlated with the Axis 1 and affected the composition and the density of rotifer community. Moreover, environmental factors related to nutrient concentrations such as total phosphorus, total nitrogen and dissolved inorganic nitrogen were also important nutrient factors which influenced the community structure of rotifer of Lake Hongze.