The karst ecosystem is a fragile ecosystem. Based on the analysis of the type and number of soil microorganisms, activities of soil enzymes, and plant community structure and its diversity in typical karst ecosystems, the main biologically microcosmic and macroscopical indexes, such as soil microorganisms, soil enzymes, plant community structure and its diversity, are put forward in the light of biological approach of ecological restoration to evaluate scientifically the fragility of karst ecosystem of Southwest China. Moreover, some reasonable measures on the harnessing of karst eco-environment were put forward based on the characteristics of fragile karst ecosystem in Southwest China.