Eutrophication brings important influence on water ecosystem. In order to understand the influence of eutrophication on the community structure of crustaceans in Lake Taihu, a comparative study on the seasonal variations of crustaceans community structure of three typical lake areas in Lake Taihu, including algae-dominated lake area (Meiliang Bay), macrophytes-dominated lake area (Xukou Bay) and strongly disturbed lake area (the lake center), was undertaken from March 2012 to February 2013. The trophic level was the highest in the lake center and the lowest in Xukou Bay. The annual average abundance and biomass of crustaceans were 199 ind./L and 1.950 mg/L in Meiliang Bay, 91 ind./L and 0.743 mg/L in Xukou Bay, and 150 ind./L and 1.557 mg/L in the lake center, respectively. Thirteen crustaceans species were identified in the Meiliang Bay, and 11 in Xukou Bay and the lake center, respectively. The dominant species of crustaceans were Limnoithona sinensis and Bosmina coregoni in the three lake areas. The annual average abundance of Limnoithona sinensis were 57, 25 and 36 ind./L, and the annual average abundance of Bosmina coregoni were 40, 22 and 32 ind./L in Meiliang Bay, Xukou Bay and the lake center, respectively. The biological diversity of crustaceans in Xukou Bay was significantly lower than that in Meiliang Bay and the lake center. Correlation analysis indicated positive relationships between abundance of crustaceans and the concentration of chlorophyll-a. It was also found that response of crustaceans to eutrophication were different in different ecological areas in Lake Taihu.