This paper is the result of environmental geological survey engineering. Objective The investigation of the geochemical behavior of heavy metals in the surface geochemical process has important guiding significance for the construction of life community of mountains, rivers, forests, fields, lakes and grasses. The purpose of this study is to investigate the geochemical behavior and driving mechanism of soil heavy metals in the middle-alpine hilly region of southwest China. It will serve the implementation of the strategy of plateau characteristic agricultural development and rural revitalization. Methods Based on 1∶250000 land quality geochemical survey data in Dayao County, Yao'an County and Nanhua County in central Yunnan Province, the source, spatial distribution pattern and driving mechanism of soil heavy metals were analyzed by geostatistics, and the driving model of soil epigenetic geochemical process of heavy metals was established in the middle-alpine hilly region of southwest China. Results The results showed that the average content of Cd and Hg in the surface soil in the study area was higher than the background value of the deep soil, Cr and Ni were higher than the background value of the soil in Yunnan province, and other heavy metals except As, Hg and Sb were significantly higher than the national background value of the soil, and local soil may have ecological risks of As, Cd and Pb. The elements of the constructed minimum dataset are As, Co, Cr, TFe, Ni, Pb, Sb, Sn, V and Zn, and the Moran index shows significant positive spatial autocorrelation. The spatial distribution features high content of heavy metals in metamorphic rocks and intrusive rocks, low content of clastic rocks and quaternary alluvium. Multivariate statistical analysis and spatial distribution characteristics of heavy metals show that Co, Cr, TFe, Mn, Ni and V mainly come from the parent material, As, Sb and Sn are greatly affected by the primary strata and metallogenic geological background, Cd, Pb and Zn are mainly affected by human activities such as industrial and mining activities. Conclusions The distribution of heavy metals is highly coupled with the ground distribution. The spatial distribution pattern of heavy metals in surface soil is controlled by geological background, and the content of heavy metals in soil varies significantly among different soil types and land use types. The vertical migration and enrichment of heavy metals are driven by rock weathering, and the heavy metal content and elevation show a significant polynomial linear fitting trend. Organic matter and pH are the main factors controlling the heavy metal behavior at different elevation intervals. Strong epigenetic geochemistry in the study area reshaped the macroscopic distribution of heavy metals. Restricted by their own chemical properties and influenced by environmental conditions (slope, pH, organic matter, etc.), distribution, migration and enrichment of heavy metals occurred in the soil. Human activities affected the distribution pattern of local heavy metals.