In order to explore the spatiotemporal variations in phytoplankton community and its influencing factors in Danjiangkou Reservoir, we conducted a one-year survey from May 2014 to April 2015. Sixty-six species, including 38 genera, 21 families and 7 phyla, were identified in the survey. The average biomass of phytoplankton is 0.35 mg/L, while the average density is 9.08×10⁵ cells/L. Dominant species are Fragilaria spp., Cyclotella spp., Melosira spp., and Scenedesmus spp.. Fragilaria spp. is the most dominant specie, and its average biomass is 0.089 mg/L, making up 25.43% of total biomass. In recent years, high level of nutrient may be the main cause of increasement in Fragilaria biomass in Danjiangkou Reservoir. Chlorophyta and cyanobacteria bloomed in summer, while diatom dominated in spring, autumn and winter. Total phytoplankton biomass in Han Reservoir is greater than that of Dan Reservoir. There were significant differences in phytoplankton composition between these two reservoirs. The dominant phylum of Dan Reservoir is Bacillariophyta, while the dominant phylum of Han Reservoir is Chlorophyta. There was significant correlation of the phytoplankton biomass with phosphorus, pH and dissolved oxygen, respectively. RDA analysis showed that the major environmental factors affecting phytoplankton community were dissolved oxygen, pH, phosphorus and temperature. For preventing the algae blooms, strict measures should be taken to control the input of exogenous nutrient especially phosphorus. This study provides scientific basis for water quality improvement and control of eutrophication at Danjiangkou Reservoir.