According to the national key research and development program of China “Evolution, integrating treatment and technological demonstration of rocky desertification in karst graben basin”, the task of “ecological, environmental and geological differentiation of rocky desertification and its driving mechanism in karst graben basin” was to reveal the migration of carbon, nitrogen, calcium and water, as well as evolution process and driving mechanism of ecosystem succession and rocky desertification. In this respect, the factors of lithology, topography, ecology, hydrology, vegetation, socio-economy, meteorology, soil, etc. were studied in the demonstration areas of Mengzi and Luxi rocky desertification control. Moreover, the interaction between vegetation and hydrological processes in the typical watershed was established, and the critical period and water requirement of the ecological water demand in the watershed were established. The ecological and hydrological process of the vegetation, as well as nitrogen, calcium and water cycling, and the carbon sequestration ability of ecosystems were used to predict the evolution of ecosystem succession and rocky desertification. The results provided the theoretical basis for the rational allocation of ecological water resources and ecological restoration in rocky desertification area.