Heavy metal pollution in farmlands is a serious threat to sustainable agricultural development and has become a major agro-ecological problem that has attracted public concern in China. This study proposes a soil-crop collaborative risk assessment model that aims to assess the potential safety risks of heavy metal pollution in farmland soils by considering the concentrations of heavy metals in soils and the accumulation effects of heavy metals in crops. Based on these effects, a decision support system for risk assessment of heavy metal pollution in farmland soil is established, in which technologies such as web-based geographic information system, quick response code, radio frequency identification, and web service are introduced as the bases. The proposed system is composed of a mobile data acquisition terminal (MDAT) and a web-based information system (WIS). The MDAT, which is a portable computerized device running on the Android platform, is used for data acquisition or query, and the WIS is used for risk assessment, data management, and information visualization. The system is employed in some county-level cities in China for risk assessment and supervision of heavy metal pollution in farmlands. The practical application results show that the system provides highly efficient decision support for risk assessment of heavy metal pollution in farmland soils.