Zhelin Reservoir is a large canyon-reservoir in the midstream of the Yangtze River, and the storage capacity is 79.2×10⁸ m³ and length is 115 km. Through measurements on a moving vessel and at fixed-point sites in the Zhelin Reservoir in April, 2015, the distribution of phytoplankton, chlorophyll-a (Chl.a) concentration and main environment variables (including dissolved inorganic nitrogen (DIN), dissolved inorganic phosphorus (DIP), dissolved silicon (DSi), water temperature, turbidity, dissolved oxygen (DO)) were analyzed. The redundancy relationship of phytoplankton taxa and environmental variables was analyzed using the software CANOCO 4.5. The results showed that, 1) the reservoir water was categorized as a middle-status in nutrients. There were 34 main phytoplankton species in the surface (the cell density of which exceeding 1000 cells/L), and the average biomass of reservoir was 0.41 mg/L. The dominant algae (dominance be equal or greater than 0.02) were the diatoms and cyanobacteria. DIN, DIP, DSi and water temperature can impact on the structure of algae, and the four factors were explained for more than 60% variation of the algal structure. 2) The reservoir had a significant phenomenon of subsurface chlorophyll maximum (SCM). The depth of SCM appears at the water depth from 3 to 8 m, and the thickness is about 2-7 m. The Chl.a in the SCM layer is 25.2%-74.1% among the total in the vertical. The algae in the SCM layer absorbed the nutrients, resulting in decreased concentrations of DIN, DIP and DSi and the increased DO concentration. 3) The reservoir had significant biological and biochemical filtering effect for the DSi. About 11% to 12% DSi were absorbed by organisms in the middle and upper area of in the reservoir, and accumulating about 21% DSi was absorbed by algae from upstream to downstream. 4) Nitrogen and phosphorus emissions by human activities have a serious impact on the ecology and water quality of the reservoir and the adjacent county region. The concentrations of Chl.a and DIP in the region is about 2.9 times and 3 times higher than that in the natural region of the reservoir, respectively.