Identifying the factors controlling the spatial variability of soil metal elements could be a challenge task due to the interaction of environmental attributes and human activities. This study aimed to investigate the critical explanatory variables controlling total Ca, Cd, Cr, Cu, Zn, Fe, Mn, Mg, Pb, and Zn variations in the arable topsoil using classical statistics, principal component analysis, and random forest techniques. The work was conducted in the core region of the Three Gorges Reservoir of China. The explanatory variables included soil, topography, climate, vegetation, land use type, and distance-related parameters. Average concentrations of the metal elements were in order of Fe > Mg > Ca > Mn > Zn > Cr > Ni > Pb > Cu > Cd. Soil Cr, Fe, and Pb showed low variability while others presented medium variability. Average concentrations of Cr, Fe, Cd, and Mg exceeded their corresponding background values. There were highly positive correlations between all metal elements except Pb, Cd and Cr. The principal component analysis further demonstrated that the sources of Pb, Cd, and Cr differed with other elements. The results of random forest suggested that soil properties followed by topography were critical parameters affecting the variations of Ca, Mg, Mn, Fe, Ni, Zn, and Cu. Agricultural activities and soil properties were major factors controlling the variations of Pb, Cr, and Cd. Further study should be conducted to understand the relations between the metal elements and soil properties.