Heavy metal pollution is a notable threat to agricultural production. Soil heavy metal pollution can cause potential ecological risk (ERI), and crop heavy metal pollution can cause human health risk (HRI). However, most previous studies partially focused on heavy metal pollution in soil or crop but often neglected the relationship between them. Actually, soil heavy metal can pollute crops to some extent, while not all heavy metal pollution in crops comes from soil. The inner relationship of pollution risk in soil-crop system is worth attention. In this study, we selected Ningbo as the study region and used sample data to assess both soil and crop heavy metal risks, in order to explore the differences between heavy metal contamination risks in soil and crops as well as the relationships between heavy metal contents in soil and crops. Our results showed that Hg was the most polluted heavy metal in soil, which led to the highest ecological risk in Jiangbei (Comprehensive ERI = 567) with the maximum ERI of Hg (430). However, As in crops contributed the most to health risk and caused the highest health risk in Fenghua (HRI = 10) with the largest contribution of 64.5%. Such differences of pollution risk assessment indicated that the contents of the same heavy metal were inconsistent in soil and crops. Our results further showed that the heavy metals in soil had the greatest influence on Zn in crops. Pb and Cr in soil had synergistic effects on the crop absorption of Zn, whereas As, Hg and Cu played antagonistic roles in the crop absorption of Zn. Our study confirms that heavy metals in soil would variously influence heavy metals in crops and the interaction of heavy metals is very important for pollution risk control, which have been largely ignored yet.