The scientific utilization of selenium (Se)-rich soils necessitates the evaluation of the contents of potentially hazardous elements (PHEs). The Menyuan Basin, a representative Se-rich region located on the northern periphery of the Qinghai–Tibet Plateau, was chosen as the research area. Pollution risk and spatial source analysis was conducted for eight PHEs (As, Cr, Cu, Pb, Zn, Cd, Ni and Hg) using 5297 topsoil samples and 480 deep-soil samples. The results show that more than 50% of the total area has a Se content >0.24 mg kg –1 . According to both single and comprehensive pollution indices, there are extremely few sampling sites with PHEs at risk of contamination. Low ecological risk was seen in 93.34% of the topsoil samples. The results show that although the overall level of surface soil pollution in the study area may be deemed negligible, on the surface or in deeper layers, the concentration centres of As, Cr, Ni, Zn, Pb and other elements show consistency, indicating that underlying parent rocks are the primary source of these elements. The findings presented in this study establish a scientific foundation for the secure development and utilization of Se-rich soils.