Conventional assessment of soil environmental quality commonly focuses on soil heavy metals (HMs), neglecting the HMs in agricultural products. To response this shortcoming, a comprehensive assessment combining both soil environmental quality and agricultural product security for evaluating soil HM impact is urgently required. This comprehensive assessment incorporates not only the HM contents in soil and agricultural product but also soil environmental quality standards, soil elemental background values, and safety standards for HMs in agricultural products. In this study, it was applied to evaluate the potential risk of HMs in soil-crop systems (i.e., soil-vegetable, soil-maize, soil-rice, and soil-wheat systems) along the Yangtze River in Nanjing, Jiangsu Province, Southeast China. Furthermore, 114Cd/110Cd isotope ratio analysis was used to identify the specific contamination sources. The mean concentrations of Cd, As, Hg, Pb, Cu, Zn, and Cr in the surface soils (0-20cm) were 0.26, 11.07, 0.09, 32.63, 38.57, and 107.92mgkg-1, respectively, exceeding the corresponding soil background values. Fertilizer and atmospheric deposition were the major anthropogenic sources of HM contamination in crop-growing soils. In addition to the crop type, soil pH and organic matter also influenced the transfer of HMs from soils to the edible parts of crops. Results of comprehensive assessment revealed that approximately 11.1% of paired soil-crop sites were multi-contaminated by HMs, among which paddy soils had the highest potential risk of HMs followed by maize soils, vegetable soils, and wheat soils. To evaluate the potential risk of HMs in arable land, this study provides a novel, scientific and reliable approach via integrating soil environmental quality and agricultural product security.