Deeply influenced by karst geological environment, the structure of the soil ecosystem in the southwest karst area of China is characterized by strong vertical variation and space variation, structural feature of nonrenewable soil, and functional feature of poor circulation of nutrient elements and limited vegetation growth. On the basis of analyzing vulnerability in structure and function of soil ecosystem in China’s southwestern karst regions, we discussed the degradation process and mechanism of soil structure, nutrient, water and microorganism in the course of soil erosion from the perspective of material and energy cycle. Finally, we put forward some recommendations for recovery of degraded soil, transformation and rational utilization of soil.