The establishment of soil geochemical baseline and heavy metal pollution assessment in the Qinghai-Tibet Plateau is of great significance for guiding environmental management in the high-cold and high-altitude regions. A total of 126 topsoil samples (0–20 cm) were collected and the contents of Cu, Pb, Zn, Ni, Cr, Cd, As and Hg were determined in the Sabaochaqu basin of the Tuotuo River, the source of the Yangtze River, in the Tibetan Plateau. The baseline values of 8 heavy metals were determined by mathematical statistics, iterative 2times standard deviation method, cumulative frequency and reference element standardization, and the soil heavy metal pollution in the study area was assessed by enrichment factor method and pollution index method. The results showed that the average contents of As, Cd, Cr, Cu, Hg, Ni, Pb and Zn were 31.84, 0.29, 66.07, 17.35, 0.021, 27.86, 49.35 and 88.56 mg/kg, respectively. Baseline values were 22.24, 0.217, 64.16, 15.69, 0.0191, 26.46, 34.91, and 68.62 mg/kg, respectively. There is a great difference between the baseline value of soil heavy metals in study area and the Xizang soil background value, especially the baseline value of Cd was 2.68 times of its background value. The results of the pollution evaluation based on the baseline values showed that the 8 heavy metals were slightly enriched, and the overall pollution status was light pollution, and measures should be taken to control and manage them. The research results can provide a reference value for the evaluation of soil heavy metal pollution in the source region of the Yangtze River, and also provide a theoretical basis for the construction of soil heavy metal baseline values in similar high-cold and high-altitude regions.