Significant enrichment of heavy metal elements occurs during the process of carbonate rocks weathering into the soil, but the factors contributing to this enrichment are not yet fully understood. This study compared the variations in heavy metal elements (Cr, Ni, Cu, Zn, Cd, and Pb) concentrations between carbonate rocks and clastic rocks, as well as their weathered soils. The findings indicate that, under the driving forces of different weathering patterns, the geochemical behavior of heavy metal elements exhibits significant differences. The enrichment and accumulation of heavy metal elements in carbonate weathered soils can be attributed to the absolute loss of mass and relative enrichment in terms of concentrations. This study further investigated the role of acid-insoluble residues in influencing the characteristics of mineral phase and migration enrichment degree of heavy metal elements in carbonate rocks through acid leaching experiments. The results demonstrate that heavy metal elements are generally inclined to be present in acid-soluble mineral phases and exhibit a distribution pattern where higher levels of acid-insoluble residues correspond to a greater tendency for heavy metal elements to be enriched in the acid-insoluble mineral phase. The migration and enrichment degree of heavy metal elements in the weathered soils of carboniferous and Permian carbonate rocks in the study area are significantly higher than those in the Cambrian system. This indicates that lower levels of acid-insoluble residues correspondingly result in more intense leaching during their weathering process. Furthermore, the concentration of heavy metal elements in the acid-insoluble residues of carbonate rocks to some extent controls the characteristics of heavy metal elements content in weathered soils. This is an important factor leading to variations in the enrichment degree of heavy metal elements in carbonate weathered soils across different geological epochs. This study provides new insights into the factors contributing to the enrichment of heavy metal elements in carbonate weathered soils. Considering the unique weathering patterns of carbonate rocks, it is recommended to prioritize the monitoring of heavy metal elements concentrations in overlying soils, surface runoff, and karst groundwater in the study area.