In order to understand the dynamic spatio-temporal characteristics of the phytoplankton community in the Danjiangkou Reservoir during high-level water storage, the species composition, density, biomass, and biodiversity of phytoplankton in the Danjiangkou Reservoir were investigated and analyzed during May, August and November, 2017, and its fish productivity was evaluated. The results showed that 114 genera (including varieties) of phytoplankton from seven phyla were recorded in the Danjiangkou Reservoir, among which Chlorophyta had the most species with 65. The average density and biomass of phytoplankton were 7.71×10⁶ ind/L and 3.37 mg/L. The total algae density of Chlorophyta, Cyanophyta, and Cryptophyta accounted for 86.31%, and each of them exceeded the density of diatom algae (accounting for 13.50%). The Margalef richness index (D_m) and the Shannon-Wiener diversity index (H′_N) of phytoplankton ranged mainly from 1 to 2, and the Pielou evenness index (J_N′ ) of phytoplankton mainly ranged from 0.4 to 0.7, with averages of 1.35, 1.78, and 0.58, respectively. The fish productivity of phytoplankton was 101.10 kg/hm² . Analysis of Similarities (ANOSIM), Permutational Multivariate Analysis of Variance (PERMANOVA), and Similarity Percentage Analysis (SIMPER) showed that there were significant seasonal differences in phytoplankton community structure in the reservoir area, which were caused by changes in the abundance of dominant species. There were no significant spatial differences in phytoplankton community composition, with a certain homogenization trend among the different reservoir areas. Compared with previous studies, our results showed that the density and biomass of algae in the reservoir had increased, the proportion of diatoms in the Danjiangkou Reservoir area had dropped obviously, and Cyanophyta and Chlorophyta algae had become the main species in the reservoir area. All phytoplankton biodiversity indexes were at a relatively lower level, which indicates that the phytoplankton community structure is simple and unstable. These results could serve as an essential scientific basis for optimizing the ecosystem structure and function of the Danjiangkou Reservoir, as well as its ecosystem health management.