Abstract: Geostatistical and multivariate analyses are effective methods to determine the source of heavy metal elements in the soil. The comparison of the contents and distribution of heavy metal elements in the topsoil and subsoil in different geological setting areas can provide a basis for studying the sources of heavy metal elements in the soil. As one of the areas with concentrated marsh wetlands in China, the Sanjiang Plain has a temperate humid and subhumid continental monsoon climate, is an important grain production base, and has a low degree of industrial activities. This study investigated the main factors affecting the distribution of heavy metal elements in the soil of cultivated land of the Sanjiang Plain on a regional scale. Samples were collected from the topsoil and subsoil of the Sanjiang Plain. The minimum, maximum, median, and average contents, coefficient of variation, and concentration coefficient of eight heavy metal elements (i.e., As, Cr, Cu, Hg, Ni, Cd, Pb, and Zn) in the samples were calculated. The results are as follows. The Sanjiang Plain has superior soil environmental quality. The topsoil samples had slightly lower contents of heavy metal elements except for Cd (e.g., As, Cr, Cu, Hg, Ni, Pb, and Zn) than the subsoil samples. All these elements in the topsoil samples had concentration coefficients less than 2, except for those in the topsoil samples collected at certain points, which had high concentration coefficients of Cd, Hg, and As elements. The main factors influencing heavy metal elements in the topsoil and subsoil in five soil parent material regions were determined through geostatistical and Pearson correlation analyses. The comprehensive analysis results show that elements Cr, Cu, Ni, and Zn mainly originate from the soil parent materials, and Cd, Hg, and As may also be affected by human activities in some areas.