Due to the lack coupling analysis of heavy metals in soil-plant-atmosphere system, the migration and transformation of heavy metals remains unclear. In this study, 240 surface (0–20 cm) soil samples, 365 plant samples and 168 atmospheric dust samples were collected in a large coal mining area, in which selected heavy metals arsenic (As), cadmium (Cd), chromium (Cr), copper (Cu), nickel (Ni), plumbum (Pb), zinc (Zn) were analyzed, to elucidate the spatial distribution and source of heavy metals and their bioavailability. According to the results of ArcGIS mapping analysis, the distribution patterns of Cd, Cu, Pb, and Zn in the three media are similar, while the distribution characteristics of Cr and Ni are highly consistent. The factors contributing to these spatial distribution characteristics of heavy metals could be associated with human activities and the characteristics of the elements. Compared with the background value, Zn, Cr, Pb in soil, Zn, Cr, Cu in plants and Zn, Pb, Cu in atmospheric dust apparently accumulated. The geological accumulation pollution index (Igeo) shows that there exist mild to moderate levels of Cr and Cd pollution in soil, and mild to moderate levels of Cd, Cr, Pb, and Zn pollution in the air. The evaluation of potential risks of heavy metals showed moderate ecological hazards in soil and strong ecological hazards in atmospheric dust. The sources of heavy metals were assessed using principal component analysis (PCA), land use type, and spatial analysis. Anthropogenic factors are the main sources of heavy metal content. Coal-related industrial processes related to coal, sewage irrigation, the use of agricultural chemicals, and vehicle emissions may be anthropogenic sources of heavy metals.