Heavy metal contamination is one of the most pressing concerns for food security and human health. Understanding the risk to human health posed by soil pollution that enters the food chain is paramount. Here, we systematically assessed potential risks due to heavy metal (Cd, Cr, Pb, Hg, and As) contamination in soil and crops (2241 pairs of soil and crop (78 species) samples) in the Pearl River Delta urban agglomeration of China. Cadmium was the most common pollutant among all the heavy metals identified in soil and crops. The greatest risk of Cd ingestion from leaf and root vegetable consumption was concentrated within Huizhou. The highest risks to human health from heavy metals were found in rice and maize. This is the first time that the risk to human health from heavy metal contamination in soil and crops, and their associated spatial risk pattern, in China have been assessed systematically.