Soil heavy metal pollution is an important content for soil environmental governance. Based on the three-Dimensional (3D) geological modeling technology and ordinary Kriging method, this study described and analyzed the soil pollution status and spatial distribution characteristics of a site in Zhongshan, Guangxi. The results showed that combining 3D geological model and the Kriging interpolation method can well evaluate soil heavy metal pollution. The 3D geological model showed that the pollutant concentration in soil ranked As>Pb>Mo and the pollution degree decreased gradually from top to bottom. As such, the miscellaneous fill soil layer was the layer that needs to be repaired. In addition, the single-factor pollution level and Nemerow comprehensive index method were used to evaluate the pollution risk of the site. The evaluation results showed that the soil quality was seriously threatened by As and the heavy pollution (Pi>3) accounted for 61.10%. Furthermore, attention should be paid to the potential risk of Pb in the miscellaneous fill layer. This study can provide a 3D visualization method for comprehensive analysis of soil heavy metal pollution and a scientific reference for the formulation and implementation of subsequent site remediation strategies.