Abstract: Phytoplankton, as an important primary producer in aquatic ecosystem, is very sensitive to the changes of water nutrient status and environment. At the initial stage of operation of the new reservoir, the changes of hydrological situation may improve the interception ability of the water body to exogenous pollutants, which easily leads to abnormal phytoplankton reproduction and even blooms. Therefore, the study on the characteristics of phytoplankton community during this period is helpful to understand the succession trend of phytoplankton community in the reservoir and provide reference for the management. Guanyinyan Reservoir and Wanying Reservoir in Liupanshui City, Guizhou Province, were newly built in 2018 and 2017, respectively. Based on field investigation, this paper studied the phytoplankton community structure and its relationship with environmental factors in the two reservoirs. A quarterly survey was conducted on both reservoirs, and the results showed that diatoms and green algae dominated the phytoplankton in both reservoirs. A total of 32 species of phytoplankton were detected in Guanyinyan Reservoir, among which diatoms and chlorophyta accounted for 31.3% and 28.1%, respectively. The average annual density of phytoplankton was 3.46×10⁶ cells/L. The total species of phytoplankton was 28 in Wanying Reservoir, diatoms and chlorophyta accounted for 35.7% and 39.3%, respectively. The average annual density of phytoplankton was 4.79×10⁶ cells/L. According to the results of redundancy analysis (RDA), water temperature, total phosphorus and transparency were the main environmental factors affecting the changes of phytoplankton communities in the two reservoirs. In general, the newly built reservoirs in this study have a low risk of algal eruption in the early stage of operation. In subsequent management, attention should be paid to the influence of temperature, exogenous nutrition and seasonal changes on phytoplankton density.