Heavy metal pollution in soil–crop systems has attracted great attention globally, caused by rapid urbanization and intensive industrialization. The research aims to investigate the environmental quality of the agricultural production area in Taizhou City, a typical economic region that is along the Yangtze River in the Southeast of China. A total of 370 sampling sites were chosen, with 370 soil, rice (Oryza sativa L.) and wheat (Triticum aestivum L.) samples collected, respectively, for measuring and analyzing the status, spatial distribution and pollution level of different heavy metals. The mean values of soil Cr, Pb, Cd, As and Hg were 66.78, 32.88, 0.23, 8.16 and 0.16 mg/kg, which were lower than the risk control standard values (RCV). However, the mean values of Pb, Cd and Hg were 1.25-, 1.77- and 2-fold larger than their soil background values (SBV) due to the intensive anthropogenic activities. The average content of Cd in rice exceeded its food safety limiting values (FCV) by 0.05 mg/kg, and the average contents of Pb in rice and wheat both exceeded the relevant FSV by 0.42 and 0.186 mg/kg, respectively. In addition, the maximum As and Cr contents in rice and wheat could be 0.13, 0.46 mg/kg and 0.63, 3.5 mg/kg larger than the relative FCVs in certain areas. Most of the high-value areas of soil and crop heavy metals were mainly located in Xinghua City, Taixing City and Jiangyan District, which had a similar distribution pattern with local industries or anthropogenic activities. The heavy metal pollution in soils and crops was found to be inconsistent, as 8.94% of the arable land possessed lightly metal pollution, while 3.18% of the area of rice and 4.0% of the area of wheat suffered severe pollution, with excessive accumulation of Cr, Pb and Cd. Based on the heavy metal pollution assessment of soil–crop systems, approximately 83% of the study area possessed medium or higher environmental quality, which was preferable for agricultural production. Our results implied that the spatial distribution and pollution level of the heavy metals in soil–crop systems were significantly influenced by industrial activities, followed by agricultural sources, transportation emissions and so on. Therefore, continuous monitoring and source control of heavy metals, especially for Cr, Pb and Cd, should be conducted to ensure the regional environmental quality and food security.