This paper is the result of environmental geological survey engineering. Objective The study area is located in an important coal and agricultural production area in eastern Yunnan Province. It is of great practical significance to understand the spatial distribution characteristics, potential ecological risks and pollution sources of heavy metals in soil of coal mining area for ecological environment protection and ensure agricultural security. Methods Based on the grid distribution point method, 497 soil samples were collected in June 2021 in typical coal mining areas, and soil pH, SOM, As, Cd, Cr, Cu, Hg, Ni, Pb and Zn were analyzed. The Pollution Load Iindex method (PLI) and the Potential Ecological Risk Index method (PERI) were used to evaluate the status of heavy metal pollution and potential ecological risks. The potential sources of heavy metals were analyzed by using Principal Component Analysis (PCA) and positive definite matrix factor analysis (PMF) models. Results The soil is mainly acidic, the average pH value of the soil is 5.39, and the average of SOM content is 1.20 times that of the background value for soils in Yunnan Province. The average and median values of Cr, Cu, Cd, Ni, Zn and Hg contents exceed the soil background values in Yunnan Province. The vast majority of sampling points have Cd, Cu, Cr, Ni content exceeding the risk screening value, accounting for 94.97%, 93.96%, 91.35%, and 79.28%, respectively. A small number of sampling points have As and Cd content exceeding the control values, accounting for 0.20% and 1.41%, respectively. The evaluation results of the PLI showed that the study area as a whole shows slight pollution. The evalution results of PERI showed that the overall risk of the study area is moderate. The results of the PCA and the PMF model analysis showed that soil heavy metals in the study area are mainly derived from the geological background, followed by agricultural activities and atmospheric deposition. Conclusion The potential ecological risks of Cd and Hg in the soil of the coal mining areas area relatively high, and the heavy metals in the soil mainly derived from the geological background, followed by agricultural activities and atmospheric deposition. It is suggested to strengthen the monitoring and management of related polluted land, reduce the unreasonable application of farmyard manure, and strengthen the supervision of pollution from coal industry activities.