Abstract: The source region of the Yangtze River, located in the central Qinghai-Tibetan Plateau, has water conservation function, and is also a natural barrier of ecosystem for the Yangtze River Basin. Meanwhile, natural ecosystem is the most sensitive, and eco-environment is very fragile in this region. As a primary producer in the aquatic ecosystem, phytoplankton plays an important role in reflecting water environment quality. To explore water environment properties and phytoplankton community characteristics in the source region of the Yangtze River, systematic surveys of water environments and phytoplankton in 10 typical sections were carried out in March 2018 and October 2018. In October, water environmental parameters such as flow velocity, turbidity, water temperature, and conductivity of the sections were all higher than those in March. These water environmental parameters such as turbidity, salinity, conductivity of the Chumaer River were significantly higher than other river segments in the same month. There was no significant difference in pH, dissolved oxygen and nitrite nitrogen among the river segments in the two months. A total of 58 phytoplankton species belonging to 4 phyla and 28 genus were identified, among which Bacillariophyta (79.3% of the total species number), Chlorophyta (10.4%), Cyanophyta (8.6%) were dominant. The variations  of phytoplankton density were 6.06×104-39.90×104 cells·L-1, the average of phytoplankton biomass was 0.59 mg·L-1 during the investigation. The dominant species were Oscillatoria formosa,Diatoma vulgare,Fragilaria sp., Synedra sp., Navicula sp., Cymbella sp., and Chlorella sp.. In March 2018 and October 2018, the Shannon-Wiener diversity means were 3.06 and 3.12, the Margalef diversity means were 1.17 and 1.52, and the Pielou diversity means were 0.90 and 0.82, respectively. Combined with nutrient indexes, phytoplankton density and diversity indexes, water quality in the source region of the Yangtze River was generally non-polluted or slightly polluted.