The carbon cycle in a global sense is the biogeochemical process by which carbon is exchanged among the biosphere, pedosphere, geosphere, hydrosphere, and atmosphere of the earth. For epikarst systems, it is the exchange of carbon among the atmosphere, water, and carbonate rocks. Southern China is located in the subtropical zone; its warm and humid weather creates favorable conditions for the dynamic physical, chemical, and ecological processes of the carbon cycle. This paper presents the mechanisms and characteristics of the carbon cycle in the epikarst systems in south China. The CO2 concentration in soils has clear seasonal variations, and its peak correlates well with the warm and rainy months. Stable carbon isotope analysis shows that a majority of the carbon in this cycle is from soils. The flow rate and flow velocity in an epikarst system and the composition of carbonate rocks control the carbon fluxes. It was estimated that the karst areas in south China contribute to about half of the total carbon sink by the carbonate system in China. By enhancing the movement of elements and dissolution of more chemical components, the active carbon cycle in the epikarst system helps to expand plant species. It also creates favorable environments for the calciphilic plants and biomass accumulation in the region. The findings from this study should help in better understanding of the carbon cycle in karst systems in south China, an essential component for the best management practices in combating rock desertification and in the ongoing study of the total carbon sink by the karst flow systems in China.