Due to the extensive development of carbonate rocks in southwest China, heavy metals are naturally occurring elements that have high natural background levels in the environment. Therefore, it is important to conduct ecological risk assessments and identify potential sources of heavy metals in the geological high background area. Based on the township scale, a total of 307 surface soil samples were collected in Qinglong Town, Fengjie County, Chongqing. The concentrations of As, Cd, Cr, Cu, Hg, Ni, Pb, and Zn and pH were analyzed and determined. The spatial distribution and source of soil heavy metals were discussed using the geostatistical analysis and an absolute principal component score-multiple linear regression (APCS-MLR) model in the studied area. The results showed that the average values of seven heavy metals (As, Cd, Cr, Cu, Hg, Ni, and Zn) in the arable soil exceeded the background values of Chongqing, and the cumulative effect of Cd and As was obvious. The concentrations of Cd significantly exceededthe screening values in The Risk Control Standard for Soil Environmental Quality and Soil Pollution in Agricultural Land (GB 15618-2018), with the over-standard rates of 52.12%. The spatial characteristics of soil heavy metal contents exhibited a pattern of high in the south and low in the north. PCA and APCS-MLR modeling revealed that the contributions of natural sources to Cr, Cu, Ni, and Zn were 86.62%, 64.34%, 76.44%, and 85.46%, respectively. As, Pb, and Hg mainly derived from industrial activities, which accounted for 74.63%, 61.90%, and 73.49%, respectively, and Cd was affected by both natural sources and industrial activities (accounting for 47.74% and 39.56% of the total Cd content, respectively). The evaluation of the soil by the Nemerow comprehensive index (P) showed that Cd pollution was relatively serious, accounting for 27.04% of soil pollution. The potential ecological hazard index showed that Cd and Hg were the main ecological hazard elements, and the distribution range of RI was 51.77 to 2228, indicating mainly mild and moderate risks, and the moderate and above risk areas in the study area were mainly located around the southern industrial source area. Altogether, our results revealed that in the study area, the heavy metal pollution was mainly caused by industrial activities, and the heavy metal pollution caused by geological background was mainly light to moderate. In conclusion, the medium and above risk areas in the study area were mainly caused by mineral and industrial activities, whereas the heavy metal pollution caused by geological background was mainly light to moderate pollution.