The traditional assessment of farmland environmental quality usually focuses on soil heavy metals, but ignores agricultural produce safety. It is urgent to comprehensively assess the effects of farmland environmental quality based on soil quality and produce safety. To fill this gap, the comprehensive assessment method was improved based on previous studies, which was used to assess the pollution level of heavy metals in soil-crop system of Shenyang, Liaoning Province, Northeast China. In addition, this study also made a comprehensive analysis of pollution sources based on positive matrix factorization (PMF) model, and discussed soil-crop system income stability by evolutionary game theory. The mean concentrations of As, Cd, Cr, Hg, Pb, Cu, Zn, and Ni in soil exceeded the corresponding Shenyang soil background values (5.68 %, 14.36 %, 57.61 %, 7.86 %, 30.32 %, 5.21 %, 211.72 %, 171.88 %). The results showed that about 28.28 % of paired soil-crop points were polluted by heavy metals, especially rice-soil points. Furthermore, heavy metals in crops may be transmitted less from soil and more from other environmental media. The PMF analysis results showed that there were six pollution sources in study area, and the major contributor of pollution were agricultural activities, traffic-related activities, and industrial activities. In farmland environment protection, the only stable strategy is soil-crop system, and soil-crop system is better than the benefits of single soil or crop from the perspective of benefits. This study provides a scientific and reliable method to combine soil quality with produce safety to assess the risk of heavy metals in farmland.