Enrichment of toxicological elements in soils of high geologic background has a significant effect on toxicity. The aim of this study was to assess the health risks associated with the transfer of toxicological elements in the food chain in a typical high geologic background. We systematically collected data on rocks, soils and food crops belonging to a typical black rock system geological body and at the same time belonging to the main grain-producing areas in Hunan Province, and analyzed the exposure and health threat of toxicological elements Cr, Cd, Pb, Hg, As and Se in cucumber, rape, soybean, peanut and ginger. Based on the JISEVM method to establish the spatial contamination constitutive relationship between rock-soil-food, we deduced the conclusions from the bioconcentration factor (BCF), integrated crop contamination index (P) and hazard index (HI). Our results showed that Cr, Cd, Pb, Hg, and Se were exceeded in agricultural soils, with Hg and Se levels severely exceeding the standard Se was most bioconcentrated in soybean (BCF = 0.5855), followed by Cd (BCF = 0.5603) and Se (BCF = 0.3800) in peanut and Se (BCF = 0.4255) in rape, and the BCFs of all the BCF of crops were less than 1, and the enrichment of these six elements in the food chain did not reach a dangerous level; the overall spatial distribution of radioactive contamination was centered on the black rocky geologic body; and the contamination and absorption levels of foods in the study area were: leafy vegetables (oilseed rape) > legumes (soybeans and peanuts) > stem vegetables (ginger) > fruit vegetables (cucumber). The intake of Cd and Se through consumption of oilseed rape was the most important source of health risk among foods in the study area. This study, since it can fill the gap in risk assessment due to endogenous factors in a high geologic background, can also guide studies in other specialized contexts or in a multi-media background.