[Objective] A land quality geochemical survey carried out in Chuxiong area of central Yunnan Province had found a large area of zinc and copper-rich soil. The purpose of this study is to study the migration and transformation mechanism of Zn, Cu and other beneficial elements in the soil-crop system in the farming area of zinc and copper-rich red bed mountain basin in southwest China. [Methods] In this paper, the typical farming area of Yao'an in central Yunnan is selected as the research area. Based on the geochemical data of surface soil and crop seed-root soil, the main control factors affecting the absorption and enrichment of Zn and Cu in rice and corn are discussed by analyzing the content characteristics of Zn and Cu in surface soil, crop seed and root soil, and the prediction model of crop Zn and Cu bioconcentration coefficient is established. [Results] The results showed that the average Zn and Cu contents in the surface soil of Yao 'an alluvial basin are 105.40 mg/kg and 42.67 mg/kg, the proportion of zinc-rich and copper-rich land (first-class) area are 84.86% and 90.59%, the average Zn and Cu contents in rice seeds are 19.28 mg/kg and 2.92 mg/kg, the enrichment rates are 100% and 70%, and the bioconcentration coefficients are 0.20 and 0.07, the average Zn and Cu contents in corn seeds are 21.42 mg/kg and 2.06 mg/kg, the enrichment rates are 80.00% and 6.70%, and the bioconcentration coefficients are 0.20 and 0.07. [Conclusions] There are differences in factors affecting Zn and Cu enrichment in rice and corn seeds. The main factors controlling Zn bioconcentration coefficients in rice are Soil-Zn, N, TFe2O3, and the main factors controlling Cu bioconcentration coefficients in rice are Soil-Cu, OM and S. The main factors controlling Zn bioconcentration coefficients in corn are Soil-Zn, SiO2/Al2O3 and TFe2O3. The multi-linear regression equation of Zn and Cu bioconcentration coefficients of rice and corn seeds in the typical farming area of the red layer mountain basin in Yunnan was established, and the optimal model decision coefficient was greater than 0.495, the prediction effect of rice is better than corn, and the prediction effect of Zn is better than Cu. The optimal model predicted that the planting area of Zn-rich rice, copper-rich rice and zn-rich corn in Yao'an County are 72.87 km2, 70.47 km2 and 69.71 km2. Therefore, the planting structure planning of rice and corn in the study area can be optimized to serve the development of plateau characteristic agriculture and the implementation of rural revitalization strategy.