As the final completion of the world-famous Three Gorges Project, the Three Gorges Reservoir(TGR) came into a normal operation stage since the year 2010, with an annual water level fluctuation of 30 m. Reservoir limnology can provide a scientific basis for environment-friendly dam construction and reservoir sustainable management. On the basis of long-term monitoring and investigation on the TGR ecosystem for 8a, this paper described the current status of aquatic environment in the reservoir, and elaborated the spatial-temporal heterogeneity of water environmental dynamics, longitudinal zonation and biological community structure, vertical distribution, and forming and tendency of algal bloom of the TGR. The early warning of algal bloom and eco-hydrological regulation mechanism were also analyzed. Two perspectives of ecological research on TGR were finally pointed out in the paper:1) Limnological observation and research in the large reservoir should have a long-term strategy; 2) Research in near future should focus on the quantification of hydrodynamics mechanism on algal bloom, and the coupling of early warning models of algal bloom and eco-hydraulic regulation platform.