Fishes, as one of the important components of wetland ecosystem, have been used as the indicator of the wetland ecosystem health. Investigation on its assemblages changes may reflect the drivers of change in the wetlands. After the operation of the Three Gorges Dam, the hydrological regime between the Yangtze River and the lakes in mid-Yangtze River basin has been changed. West Dongting Lake has been directly impacted by the operation of the Three Gorges Dam due to its close hydrological connections with the Yangtze River. To monitor the changes of fish community structure at West Dongting Lake and analyze the causes of the changes, we conducted two surveys, of which the first one was before the operation of Three Gorges Dam, from September 2002 to August 2003;and the second one was after the operation of Three Gorges Dam, from July 2012 to February 2014. In total, 91 fish species were identified, which belong to 7 orders and 17 families. The most specie-rich order was Cypriniformes (58 species), accounting for 63.7% of all species identified. According to the survey results, the number of fish species at West Dongting Lake declined from 85 to 66;the diversity index of Shannon-Wiener declined from 5.00 to 1.11, while the evenness index of Pielou declined from 4.14 to 1.00. Body size of all fishes became smaller after the operation of the Three Gorges Dam. The structure of fish communities were also changed both in the dominant species and assemblages composition. The dominant fish groups include bottom feeders, settling fishes and omnivorous fishes, and its proportions in the assemblages have been increasing. We observed decline in the proportions of carnivorous fishes, pelagic fishes, semi-migratory fishes, and fishes that laying adhesive egg, as well as demersal eggs, among which, pelagic fishes declined significantly. The species diversity in West Dongting Lake declined after the operation of Three Gorges Dam. Our results reveal that habitat loss and over fishing are major threats to the survival of some specific fish groups and have been reflected in the changes of the fish community structure.