Urban river-lake connections in different hydrological characteristics waters result in a diverse aquatic environment, which provides heterogeneous habitat conditions and contributes to increase zooplankton diversity. To understand the effects of connectivity and heterogeneity on the rotifer community structure of Lake Liuye and its adjacent waters in Changde city of Hunan, we conducted the survey quarterly on the rotifer community structure and environmental characteristics at 15 sampling sites in Lake Liuye, Chuanzi River and the Changde section of the Yuan River in 2018. During our investigation, the trophic status in different waters decreased in the order: Chuanzi River > Lake Liuye > Yuan River. The Chuanzi River and Lake Liuye were eutrophic, and the Yuan River was mesotrophic. A total of 88 rotifer species (including 8 subspecies and 1 varietas) were recorded. Polyarthra dolichoptera was the dominant species in this system. The highest abundance of rotifers reached 2535 ind./L, and the spatial distribution of annual average abundance decreased in the order: Lake Liuye > Chuanzi River > Yuan River. The temporal distribution of abundance decreased in the order: June > September > March > December. The composition of rotifer species was similar among the three waters with the same first dominant species, while the annual average abundance and diversity indices varied according to spatial heterogeneity. Canonical correspondence analysis indicated that water temperature was the key factor to the variation of rotifer community structure.