The year 2020 is the first year of the 10-year fishing ban in the Yangtze River. As an important ecological barrier of the Yangtze River, the water ecological environment health of the Three Gorges Reservoir (TGR) is of great significance to the implementation of the Yangtze River protection. Nineteen sites were set in the main and tributaries of the TGR in year 2020 (August and November) and 2021 (January and April) to explore the composition of phytoplankton community, and multiple assessment methods such as biomass, diversity index, comprehensive trophic status index and phytoplankton Q index were used to evaluate the water ecological health of the TGR area and analyze its influencing factors. The results showed that: (1) The 266 taxa of phytoplankton belonging to 105 genera in 8 phyla were identified,the average annual density was 6.4×10⁴ cells/L and an average annual biomass was 0.038 mg/L. The composition of dominant species varied seasonally. Melosira varians Agardh, Skeletonema spp. and Fragilaria spp. were the dominant species all year round. (2) The phytoplankton in the TGR was classified into 24 functional groups, of which B, D, MP, S1, P and Y were the dominant functional groups. Redundant analysis showed that Cond, total nitrogen, COD, total phosphorus, pH and total dissolved solid were the main environmental factors affecting the functional groups in the TGR. (3) Compared with the assessment results of density, biomass and the diversity of water quality, phytoplankton Q index were more suitable for the assessment of water ecology in the TGR. Results showed that the water ecological environment of the main stream in the TGR area was generally good. However, the significant increases of the density, biomass and the decrease of phytoplankton Q index in spring and summer tributaries would affect the water ecological health of the main stream to a certain extent, which had become the main risks for the TGR area. Therefore, we should make full use of the monitoring and early warning of tributary bloom and take advantage of the water ecological dispatch of the main stream to ensure the water ecological environment health of the whole TGR area.