Three Gorges Reservoir (TGR) is the key project for the governance and development of the Yangtze River. TGR is an important region for the ecological and environmental protection in the Yangtze River economic belt. The hydrology and water environment have taken fundamental changes since the impoundment of TGR with some negative ecological and environmental problems. To address whether the aquatic ecosystem of TGR is healthy or not, the phytoplankton community index (PhyCoI) was used to assess the ecosystem health of TGR. Field survey was carried out on April 2015 in the whole region of TGR, including 23 tributary bays and 18 sections in the main channel of TGR with 173 sampling sites. A total of 61 phytoplankton taxa were identified, belonging to Cyanophyta, Chlorophyta, Bacillariophyta, Cryptophyta, Pyrrophyta, Euglenophyta, and Chrysophyta. Based on the scores of PhyCoI, the overall health status of TGR is good, with 68% sites in the status of very healthy (4≤PhyCoI<5) or healthy (3≤PhyCoI<4), 26% sites in sub-healthy (2≤PhyCoI<3), and 6% sites in general sick condition (1≤PhyCoI<2). Specifically, 96% sites in the main channel of TGR are healthy, and other 4% sites are in the status of sub-healthy. In the tributary bays, the ratios for the status of very healthy, healthy, sub-healthy, and general sick are 2%, 53%, 35%, and 9%, respectively. From the view of spatial distribution, overall health status of the main channel of TGR is good, and the health status of the main channel in Hubei Province is better than that in the Chongqing Province. In addition, the health status of sites in the Xiangxi Bay, Meixi Bay, and Xiaojiang Bay were highly variable. And in general, the health status of the bays near the dam of TGR is better than the bays far away from the dam. These results provide science and technology support for ecological and environmental protection of TGR.