Based on field data and using space-for-time substitution, we discussed how phytoplankton community in lakes responds to mitigating eutrophication. Our field survey and sampling was conducted in five sub-lakes of East Lake in Wuhan:Lake Guozheng, Lake Tangling, Lake Tuanhu, Lake Miaohu, and Lake Shuiguo. The comprehensive trophic state indexes indicated the five sub-lakes were in distinct trophic states, within the range between 45.4 and 76.8. Moreover, the phytoplankton density and biomass were in the range of 2.03×10⁶ to 245×10⁶ cells/L and 0.819 to 19.9 mg/L, respectively. Results from representational difference analysis showed that the succession of phytoplankton species were significantly related to water temperature (WT), total nitrogen (TN), transparency, total dissolved solids and ammonia nitrogen. We further analyzed the casual relationships between abiotic environmental variables and phytoplankton density/biomass using stepwise multiple liner regression. It was found that TN and WT were the main factors affecting phytoplankton density. Meanwhile, phytoplankton biomass could decrease with the reduction of TN and total phosphorus. Although the total density and biomass of phytoplankton showed a decline with eutrophication mitigation, there was no obvious response in their species composition and biodiversity. Additionally, we found phytoplankton biodiversity and trophic levels showed nonlinear relationship. Therefore, to restore the degraded lakes, short-term and long-term interventions are both needed. Additionally, we should pay more attention to recover biodiversity and ecosystem functions.