The upper reaches of the Heihe River have been regarded as a hotspot for phytoecology, climate change, water resources and hydrology studies. Due to the cold-arid climate, high elevation, remote location and poor traffic conditions, few studies focused on heavy metal contamination of soils have been conducted or reported in this region. In the present study, an investigation was performed to provide information regarding the concentration levels, sources, spatial distributions, and environmental risks of heavy metals in this area for the first time. Fifty-six surface soil samples collected from the study area were analyzed for Cr, Mn, Ni, Cu, Zn, As, Cd and Pb concentrations, as well as TOC levels. Basic statistics, concentration comparisons, correlation coefficient analysis and multivariate analyses coupled with spatial distributions were utilized to delineate the features and the sources of different heavy metals. Risk assessments, including geoaccumulation index, enrichment factor and potential ecological risk index, were also performed. The results indicate that the concentrations of heavy metals have been increasing since the 1990s. The mean values of each metal are all above the average background values in the Qinghai Province, Tibet, China and the world, except for that of Cr. Of special note is the concentration of Cd, which is extremely elevated compared with all background values. The distinguished ore-forming conditions and well-preserved, widely distributed limestones likely contribute to the high Cd concentration. Heavy metals in surface soils in the study area are primarily inherited from parent materials. Nonetheless, anthropogenic activities may have accelerated the process of weathering. Cd presents a high background concentration level and poses a severe environmental risk throughout the whole region. Soils in Yinda, Reshui daban, Kekeli and Zamasheng in particular pose threats to the health of the local population, as well as that of livestock and wildlife.