Heavy metals (HMs) pose a significant threat to soil quality, plant growth, and human health. However, the impacts (transport, pollution, and health risk) of HMs in medicinal and edible plants with rich value growing in high background soil for a long time remain unclear. So the effects of HMs on the "soil-medicinal and edible plant-human" system were comprehensively studied. Houttuynia cordata Thunb. (HCT) and growing soil were collected from the farmland around Beiya mining area located in Three Parallel Rivers of Yunnan Protected Areas, China. The transport, pollution, and health risks of HMs in the system were investigated by determining the content of active ingredients, HMs, and physicochemical properties in HCT and soil. The results of comprehensive analysis using various measurement and analysis methods showed that Zn, Cu, Mn, and Co in soil could affect the contents of available nutrients (available P (AP), available K (AK), and organic matter (OM)), while AP, OM, pH, Co, and Fe in soil were closely related to the formation of HCT quality. Cr and Fe had the strongest transport capacity in stems and leaves of HCT, respectively. Furthermore, it is worth noting that Cr, Pb, and Cu had caused serious pollution to HCT in the area. Pb and Cu are tolerable levels for human health and may pose a carcinogenic risk. Our study demonstrates that HCT is expected to be a marker of heavy metal pollution in the area and provides a scientific basis for making effective regulations on HMs control and scientific planting.