The rocky desertification is the most seriously eco-environmental problem in karst regions, Southwest China. The local and national Chinese governments have being implemented a series ecological restoration projects to combat and control rocky desertification. The decrease of rocky desertification in karst peak-cluster depression regions is relatively faster than other karst landforms. However, the treatment of rocky desertification still faced the extensive investment and subregion, the lack of regional pertinence for treatment technology and model, and low comprehensive benefits. Therefore, it should be paid more attention to enhance the ecosystem services in combating and controlling rocky desertification in karst peak-depression regions, including the area increase of rocky desertification. One of the National Key Research and Development Programs has been supported by the Ministry of Science and Technology of China (Grant No. 2016YFC0502400). This program aimed to enhance the ecosystem services of karst peak-cluster depression. Firstly, this program explores the mechanisms of rocky desertification evolution on regional scale, the regulation and control of water and soil loss and drop out processes, vegetation recovery and human-driven enhancement of soil ecological functions. Then, it will research and develop the adaptively ecological restoration and reconstruction technology related to the function optimization-oriented ecosystem monitoring and assessment, the regulation, storage, and efficient utilization of epikarst water, the utilization of organic materials and improvement of degraded soil fertilities, the construction and assembly of drought-enduring vegetation communities and large-scale plantation, the cultivation and development of ecological derived industries. At last, with the integration and demonstration of adaptive restoration technology, the program will propose systemic solutions to accomplish the synergies of ecosystem services enhancement and livelihoods improvement for the comprehensive treatment of rocky desertification. This implementation of this program will provide scientific foundations and demonstration prototype for the implementation of karst rocky desertification management and control project and poverty relief.