When creating a soil contamination map using geostatistical techniques, there are various sources that can affect prediction errors. In this study, a grid-based soil contamination map was created from the sampling data of heavy metal concentrations in soil in abandoned mine areas using Ordinary Kriging. Five factors that were judged to affect the prediction error of the soil contamination map were selected, and the variation of the root mean squared error (RMSE) between the predicted value and the actual value was analyzed based on the Leave-one-out technique. Then, using a machine learning algorithm, derived the top three factors affecting the RMSE. As a result, it was analyzed that Variogram Model, Minimum Neighbors, and Anisotropy factors have the largest impact on RMSE in the Standard interpolation. For the variogram models, the Spherical model showed the lowest RMSE, while the Minimum Neighbors had the lowest value at 3 and then increased as the value increased. In the case of Anisotropy, it was found to be more appropriate not to consider anisotropy. In this study, through the combined use of geostatistics and machine learning, it was possible to create a highly reliable soil contamination map at the local scale, and to identify which factors have a significant impact when interpolating a small amount of soil heavy metal data.