The agricultural soil in China has been widely polluted by heavy metals and the regional contamination is serious. The experience on soil remediation in developed countries is significantly instructive for farmland protection in China. The heavy metal pollution of farmlands in China faces great challenges including spatial heterogeneity of heavy metal accumulation, various enrichment characteristics depending on soil types and crop, soil acidification, loss of soil trace elements, unreasonable development patterns, significant input of heavy metal into soil, poor correlation between the heavy metal concentration in soil and crop plants, inadvisable remediation techniques, and lack of long-term risk control measures. Responses to these problems, we proposed a soil prevention and control system to promote the remediation of contaminated cropland in China, which mainly focused on pollution prevention, and take prior protection as well as risk control as basic course. Based on this system, the soil pollution prevention and control work can be implemented through systematically procedures including soil environment investigation, pollution source control, risk assessment and classification management, and the derivation of soil quality threshold.