Taking Qianjiang District of Chongqing City as an example, this paper studied the source, associated relationship and crop absorption of soil Cd and Se in the high geological background area. The results showed that soil Se resources were abundant in the study area, the proportions of soil Cd exceeding the selected value and the controlled value were 30.81% and 1.74%, respectively, and soil was mainly acidic. Soil Se and Cd contents were mainly affected by the distribution of Permian, Devonian and Cambrian strata, and in Silurian strata, agricultural activities had a certain influence on soil Cd content. The associated and surface enrichment of Cd and Se in soil were obvious, which may be related to the adsorption of clay minerals, organic matter and Fe/Mn oxides in soil. The contents of Fe and Mn oxides and organic matter in soil inhibit Cd and Se absorption in rice, and soil pH is a key factor affecting the absorption of Cd and Se in rice. Alkaline conditions could reduce Cd absorptionand and promote Se absorption by rice. Therefore, the regulation of soil pH is key to the safe development of Se-rich resources.