<p>The effects of human activities on heavy metal pollution in agricultural soils have been less investigated on the Qinghai-Xizang Plateau. The present study was designed to assess the potential sources and contamination risks of heavy metals (Cr, Cd, Pb, As and Hg) in agricultural soils in three typical agricultural counties in the Huangshui River Basin of the Plateau, a total of 520 samples of agricultural soil were taken from the surface over two years. Heavy metals data were systematically analyzed by GIS mapping, positive matrix factorization (PMF) and risk assessments methods. The results showed that the heavy metal concentrations in the soil of all three counties were below the risk screening value of soil contamination of agricultural land in China. The main source pathways of heavy metals were identified based on the PMF model, with Hg as atmospheric deposition, Cr, Pb, and As as soil parent materials, and Cd as fertilizer application and industrial activities. Cr, Pb, and As exhibited no contamination and posed low ecological risk due to minimal accumulation, while posed a carcinogenic risk through oral intake; some of the sample sites for Cd and Hg had high concentrations and posed some ecological risk, but there was no health risk from any exposure. The integrated assessment of multiple risk assessment methods is more conducive to pollution risk control of heavy metals. Reduction of Cd and Hg should be recognized as an important component of soil pollution management strategies and action plans for cultivated soils.</p>