The Jilantai Salt Lake Basin in the northwest inland area of China was selected as the study area. A total 120 soil samples from soil surface, 50 and 100 cm depth were collected to test for Cr, Hg, As, and the concentration of the main chemicals. The spatial distribution characteristics of Cr, Hg, and As were identified through geo-statistical interpolation. The pollution degree, pollution distribution, and ecological risk of Cr, Hg, and As were analyzed by a single factor index method, Nemero index method, and a potential ecological risk index. A source analysis of Cr, Hg, and As was performed by a statistical correlation test and a principal component analysis. There were similar spatial distribution characteristics for the concentrations of Cr, Hg, and As in the soils of the Salt Lake Basin. Cr was higher in the Bayinwula mountain area, the Wulanbuhe desert area, and the hilly area of the southwest study area; Hg was higher only in the northeast local area and the hilly area of the southwest study area; and As was higher in near the lake, the Helan mountain area, the Bayinwula mountain area, and the Wulanbuhe desert area than in the other areas. Based on the background value of soil quality for inner Mongolia, the order of soil pollution is As > Hg > Cr, in which Hg and As was at a moderate level of pollution above the cumulative proportion of 45%, but Cr was only at a slight level of pollution at 7.5%. There was no clean soil in the study area; cleaner soil only accounted for 2.5%. The beginning stages of contamination to moderate pollution in the soil are above 50% and 42.5%, respectively. The soil risk order is Hg > As > Cr. Broadly for the study area, Hg was at a very strong ecological risk level. A slight ecological risk accounted for 40%. Moderate to strong risk were within 20%. Most areas were in a slight ecological risk situation. Based on the Chinese national standard value of soil environmental quality and the assessment results from the single factor pollution, comprehensive pollution, and the potential ecological risk index, Cr, Hg, and As in the soil do not appear in a polluted area. Although there is no Cr, Hg, and As pollution or potential ecological risk, the concentration of Cr, Hg, and As in the study area soil from inner Mongolia was higher than that in the other areas. In the study area, Cr may be mainly derived from a natural source of soil parental formation, where Hg and As may be mainly derived from industrial emissions, traffic pollution, and other human-related activities. All the heavy metals are subject to integrated impacts from human activities and changes to the natural environment.