Karst rocky desertification has become a very significant issue in ecological and geological environments, and it seriously restricts the sustainable development of society and economy in Southwest China. Rehabilitation and restoration of karst rocky desertification have become very important for the society and economy of China. Soil organic carbon is an important parameter used for evaluating soil quality. It can indicate the status of land productivity and environmental health. Soil organic carbon is the main factor for the carbon balance of a terrestrial ecosystem and can indirectly affect the terrestrial biological carbon pool. Changes in the transformation and accumulation of soil organic carbon can directly affect the dynamics of the global carbon cycle. Thus, soil organic carbon has become a research hotspot in the field of ecology. In the present study, first, we systematically summarized the spatial and seasonal distribution characteristics of soil organic carbon among different land cover/land use and different rocky desertification degrees of the karst rocky desertification ecosystem in Southwest China. Second, on the basis of previous studies and field surveys, we deduced the influence factors, including natural and human factors such as climate, landform, soil properties, vegetation cover, land cover/land use change, and agricultural management practices, related to the distribution of soil organic carbon. Finally, we proposed measures to improve the soil organic carbon content of the karst rocky desertification ecosystem. Our results can offer an important scientific basis for the rehabilitation and restoration of karst rocky desertification and rational soil utilization in the karst rocky desertification ecosystem and improve soil carbon sequestration to increase the carbon sink in the global carbon cycle.