The karst landscape in China are mainly located in the southwest of China around Guizhou province and cover an area of 550 000 km². Southwest China is most famous in the world for the continuous distribution of karst landscape, for holding the largest area of bare carbonate rocks and for experiencing the strongest karst development in the world. The karst area in southwest China is characterized by unique geological background, high landscape heterogeneity, low ecological capacity. In the meanwhile, this region is populous and in turn the exploitation of natural resources has been very high. For example, most natural vegetation has been converted to croplands. As a consequence, the region has experienced serious soil erosion or rocky desertification over the past decades due to the fragile nature of the ecosystems here, which posed great threat on the sustainable development of this region. In addition, since southwest China is located in the headwaters region of the Pearl River and Yangtze River, the ecological degradation in this region directly impacts the ecological safety the in the middle or lower reaches of the two rivers' watersheds. Therefore, a comprehensive control of the karst rocky desertification and an effective restoration of the degraded areas are necessary for ensuring the ecological security of the Yangtze and Pearl rivers' watersheds. In this paper, we systematically synthesized the information regarding rock desertification in the karst area in southwest China obtained largely from but not limited to Huanjiang Observation and Research Station of Karst Ecosystem, Chinese Academy of Sciences. We proposed a new definition of rocky desertification and its classification criteria. Based on remote sensing data, we discussed the spatial distribution and dynamics of rock desertification in the karst area in southwest China. At different stages of rocky desertification, the ecosystems were related to different characteristics embodied by a combination of vegetation, soil physics, chemistry, and microorganism. The occurrence of karst rocky desertification was explained from natural factors (e.g., geological factors) and human activities, especially agricultural activities. We proposed several regulation strategies according to the degree of rocky desertification to boost the harmonious and sustainable development of ecology, economy and society in the karst areas of southwest China.