The agricultural land-atmospheric dustfall-plant system around the mining area is at high risks of heavy metal pollution caused by mining-smelting activities. In this study, 118 samples (including rhizospheric soils, background soils, soil-forming parent rocks, crops, vegetables, medicinal plants and atmospheric dustfall) were collected nearby Tongling Cu-Fe-Au mining area, Eastern China. We studied the concentrations, migration, sources, and health risks through consumption of two main crops (corn and rice), six kinds of vegetables, and medicinal plants (Fengdan, Paeonia ostii) for six metal elements (Cu, Zn, Cr, Cd, Pb and Hg). Results revealed Cr and Cd in soils, and Cd, Cr, Pb, Cu and Zn in dustfall showed a relatively high contamination degree. The mean contents of Cr and Pb in corn kernels, as well as Cd, Cr and Pb in rice grains and all vegetables, and Cr in Fengdan cortex moutan exceeded the corresponding food safety limits in China. The transfer capability of Cr in corn kernels and rice grains, Pb in edible vegetables, and Cd in cortex moutan were the strongest, respectively. Health risk assessment results showed Cr had the greatest non-carcinogenic risk, followed by Pb and Cd. The results of pearson's correlation analysis (CA), hierarchical cluster analysis (HCA), and principal component analysis (PCA) indicated Zn-Cr, Pb and Cd-Cu-Hg in the plants might derive from different geochemical end-members. Source apportionment based on lead isotope showed that mining-smelting activities were the major source of Pb in atmospheric dustfall and agricultural soils, with the average contribution rates of 66% and 50%, respectively. Vehicle emissions from diesel fuels (50%–68%) and mining-smelting activities (16%–25%) contributed mainly to Pb accumulation in plants. Hence, our study suggested the accumulations of Pb in plants might be mainly from the direct foliar uptake of atmospheric Pb related to vehicle emissions and mining-smelting activities.