The study of the control of geological background over soil elements could provide a scientific basis for regional soil element geochemical research, planting fertilization and agricultural layout. This paper discusses the influence of the geological background on the content and distribution of Cl, Mn, B, Zn, Cu and Mo by using the grid location and chemical analysis, combined with the GIS technology and the related evaluation standards. According to the results, the values of Mn, Cu and Zn are generally moderate and at rich level in Yubei area; Mo and B element values are moderately high and are significantly higher than the values of the main urban area of Chongqing; Zn element values are significantly higher than the national level. B, Cl, Cu and Mn elements show a high degree of spatial correlation, with structural spatial variation playing a leading role, affected by the geological background. Mo and Zn elements show moderate spatial correlation, influenced jointly by structural factors and stochastic factors. The strata play a dominant role in the distribution of elemental content, and the distribution of soil element content corresponds spatially to the strata. Soil parent rock determines soil elements content level, with the main affecting factor being rock type and the subordinate factor being the geological period of the formation of the rock . These features further explain the impact of strata on soil elements. The influences of soil type on elements are also significant. The content of Mn, Cu, Zn, Mo, B is highest in the limestone soil, and the content of Mo is the lowest in paddy soil. These results indicate that the study of the control of geological background as the dominant factor over soil elements can provide the basis for the study of the planting fertilization and agricultural distribution planning.