We evaluated the response of a rotifer community to environmental changes in five shallow lakes in the middle reach of the Changjiang (Yangtze) River in summer and autumn 2010. These five lakes differed in trophic status and rotifer community structure. Twenty-nine rotifer species were collected, of which Keratella cochlearis, Polyarthra dolichoptera, and Trichocerca elongate were dominant. The mean density, Shannon-Wiener diversity, and equitability among the five lakes differed significantly (P < 0.05). The mean rotifer density was positively correlated with trophic state. The diversity was higher in lakes with high macrophyte coverage. The composition of rotifer species was closely associated with the trophic gradient. Five environmental variables, Secchi depth, conductivity, TN, NH4-N, and TP, significantly affected the composition of rotifer species. Keratella quadrata, Brachionus calyciflorus, and B. forficula were more common in eutrophic conditions. Our results suggest that eutrophication has a significant influence on the rotifer community structure and highlight the potential for using rotifer community structure as an indicator of trophic status in subtropical lakes.