Previously risk evaluation did not consider soil composition and the in–situ existing forms for heavy metals in soils would be altered during sequential extraction. It necessitates exploring the detoxification pathways of heavy metals using real soil biological/non–biological components and then linking them to risk evaluation of heavy metals. In this study, we focused on the potential health risks associated with heavy metals, enzyme/extracellular polymeric substances (EPS)–producing bacteria associated with heavy metal resistance, and non–biological compositions in soils from typical copper producing areas throughout China. This study showed that 83% of the monitored regions in 7 provinces throughout China posed unacceptable health risks using prediction models. Details include Pb (1.21) and Hg (3.60) with unacceptable non–cancer hazards, As (1.44E-04) with unacceptable cancer risks, and highly unacceptable risks associated with groundwater ingestion from soil leaching. The production processes and periods as well as ore composition accounted for the distributions of heavy metals in soils through principal component analysis. Linkage between heavy metals, soil biological and non–biological components were built using redundancy models. Based on the results, two possible existing forms were revealed for detoxification of heavy metals. First, the ternary complex of heavy metal, phosphate and Fe (hydr)oxide were formed for multiple metals, where the urease and catalase were up–regulated. Second, the bacterial EPS complexed with Fe (hydr)oxides was formed in soils with Cr of low risks and high total N/total P ratios. Therefore, we recommended insight into pollution sources and existing forms of heavy metals to control risks.