Currently, freshwater ecosystems are suffering from eutrophication and climate warming. We enumerated both direct and indirect effects of eutrophication and climate warming on phytoplankton communities of freshwater lakes. It was indicated that climate warming might alter algae biomass or community structure through influences on physic-chemical properties, aquatic plants composition and food-chain structure. We further analyzed potential mechanisms of cyanobacterial-blooms by comparing diversified responses of different lakes to climate warming and eutrophication. The results demonstrated that eutrophication and warming played similar roles in affecting lake ecosystems. Both eutrophication and warming promoted regime shift from clear-water state to turbid ones and accelerated the increase of cyanobacterial biomass and bloom intensity. However, the relative contribution of the two factors on biomass was dependent on lake types (Hierarchical or Hybrid), trophic level and phytoplankton community structure. Finally, we suggest that further studies on responses of phytoplankton functional groups to eutrophication and warming are necessary and obligatory.