Guangxi Zhuang Autonomous Region is a province of karst developing very widely and intensely, with intense soil erosion intensity and fragile eco-environment. Based on the extensive factors, this article set up an evaluating index system of fragile eco-environment and established the process of the quantitative evaluation. The process includes the set up of a database, and the determination of assessment unit, assessment indicators as well as their weights, and evaluation methods for fragile eco-environment. With powerful input, spatial analysis and mapping functions of GIS, the methods including geographic data grouping and cluster analysis are adopted, quantitative assessment and qualitative assessment are performed for fragile karst eco-environment, in order to provide the scientific foundation for eco-environment construction of the karst Guangxi area.