Chinese government is doing increased efforts to protect ecosystems. The area of rocky desertification in Southwest China karst is undergoing continuous net reduction with the strengthening measures for the comprehensive control of rocky desertification treatment. Thus, the social and ecological conditions of this area are transforming from the previous high pressure of human disturbance to large-scale natural recovery and artificial afforestation. Hence, changes in rocky desertification treatment are also required. Given the need for scientific methodology and technical support for the comprehensive treatment of rocky desertification, current studies have revealed the degradation mechanisms of human disturbances to the fragile karst ecosystem, and conducted preliminary exploration of the restoration mechanisms of ecosystem structure and function improved by ecological management. On the basis of these studies, breakthroughs have occurred in the water and soil conservation and adaptive vegetation recovery technologies and measures for rocky desertification treatment. The effects of conservation and restoration on increased vegetation recovery and carbon sequestration in China karst areas that have been identified. In terms of the sustainability of karst ecological restoration, however, rocky desertification treatment faces new problems, such as the difficulties in the consolidation of ecological restoration and poverty alleviation, the lack of technology and measures targeted to karst ecosystem, the improvement for structures and functions of widely inefficient plantations, and the human factors behind the ecological restoration of karst ecosystem. Therefore, ecological conservation and restoration in China karst should focus on improving the quality and efficiency of rocky desertification treatment, pay more attention to the transformation from a single ecosystem component and process to the combination and integration of multiple components and processes, and couple the surface and subsurface processes of karst ecosystem, landscape patterns and processes, ecosystem processes and services, natural and social processes. The future karst ecology research will provide the scientific foundation for the consolidation of rocky desertification treatment and poverty alleviation, and the implementation of Beautiful China and Rural Revitalization strategies.