We investigated the weathering-pedogenesis of carbonate rocks and its environmental effects in subtropical regions of China. The investigation demonstrated that the weathering-pedogenesis of carbonate rocks is the process of a joint action of corrosion and illuviation and metasomatism in subtropical region. It is characterized by multi-stage, multi-path and multi-style. With the persisting development of weathering-pedogenesis of carbonate rocks, metasomatic pedogenesis progressively became the main process of the weathering-pedogenesis and the dominant style of formation of minerals. And it proceeds through the whole process of evolution of the weathering-pedogenesis of carbonate rocks. The stage evolution of weathering-pedogenesis of carbonate rocks and the fractionation evolution of newly produced minerals are characterized by obvious vertically zoning structures and the rules of gradation of elements geochemical characteristics in the carbonate rocks weathering profiles. The geochemical process of weathering-pedogenesis of carbonate rocks can be divided into three geochemical evolution stages, i.e., the Ca, Mg-depletion and Si, Al-enrichment stage; the Fe, Mn enrichment stage and the Si-depletion and Al-enrichment stage in the subtropical regions. Consistent with the three geochemical evolution stages, the sequence of formation and evolution of minerals can be divided into the clay mineral stage; the Fe, Mn oxide and the gibbsite stage. The influence of weathering-pedogenesis of carbonate rocks on the chemical forms of heavy elements is mainly affected via newly produced components and minerals in the process of weathering-pedogenesis, e.g., iron oxide minerals and organic matters. The important mechanism for the mobilization, transport and pollution of F and As is affected the selective adsorption and desorption of F and As on the surface of iron oxide minerals in the subtropical karst zones, i.e., the selective adsorption and desorption on mineral surfaces of newly produced minerals in the process of weathering-pedogenesis control the geochemical behavior of elements on the Earth’s surface and environmental quality in subtropical regions.