This study investigated the spatial, vertical and fraction distribution, multivariate statistical analysis, as well as assessed pollution levels and health risks posed by heavy metals at the Wenshan mining area. There were 6 sampling points at the site, from which a total of 32 samples were collected. The eastern and south-eastern parts of the site were heavily polluted, while the western and north-western parts were less contaminated. As pollution was particularly severe in the topsoil, with the mean value of 503.31 mg kg− 1 being more than 25-fold higher than the risk screening value. As content in all layers was greater than the standard risk screening value in the three typical profiles. The proportion of various Ni, Cu and As fractions changed slightly with depth at all three sampling points, and the residual fraction percentage accounted for more or nearly 80% of the total concentration. In addition, a significantly negative correlation (p < 0.05) was detected between Ni and As (-0.85), indicating a different source of these two elements. Principal component analysis demonstrated that two PCs, i.e. PC1, attributed to human activities, e.g. mining activities and transport, and PC2, defined as natural sources, were responsible for 80.632% of the total variance. As posed severe ecological and unacceptable health risks, i.e. non-carcinogenic and carcinogenic risks both for adults and children. Therefore, a comprehensive understanding of the characteristics of mining pollutants and improved emission management in the mining process are essential to protect the environment and health of local residents.