Daphnia carinata is a large zooplankter in many eutrophic lakes and has a high efficiency to graze phytoplankton. The effects of Daphnia carinata on chlorophyll-a and the community structure of phytoplankton of Lake Xuanwu in Nanjing was studied experimentally. The results showed that the density of phytoplankton decreased 83% and the chlorophyll-a decreased 81% in the Daphnia carinata treatment comparing with the control. There is no significant relationship between nitrogen, phosphorus and chlorophyll-a in the Daphnia treatment. When Daphnia presented, the community structure of phytoplankton had changed. The proportion of Cyanophyta, Chlorophyta and Bacillariophyta obviously increased and the proportion of Cryptophyta obviously decreased. The Chrysophyta, Pyrrophyta, and Euglenophyta were not found at the end of the experimentation. Our experiments showed that Daphnia carinata can efficiently control the biomass of phytoplankton and change the community structure of phytoplankton.