Abstract: The loss and damage of soil and water resources caused by rocky desertification has become a serious problem of limiting the economic development in Guangxi region of southern China. To establish a set of evaluation index system of Guangxi, which can scientifically and reasonably evaluate the effect of soil and water conservation in this region, has important significance for the development of soil and water conservation work in Guangxi area.According to the unique characteristics of rock desertification such as exposed bedrock, slowly grown soil and difficult vegetation growing in Guangxi region, we summarized a primary index system which was composed of 9 categories, including ecological effect, economic effect and social effect based on “Soil and Water Conservation Benefit Calculation Method” (GB/T 15774—2008), integration of hydrological station data, county, yearbook and other historical data provided by Guangxi Water Resources Department. Dimension of index was reduced by principal component analysis, then we analyzed the major pathway of each index in principal components combined with the results of correlation analysis, path analysis and sensitivity analysis. Sensitivity of indices was tested and redundant indices were deleted in order to get a dimension reduction index system, which has a strong representation covering more comprehensive content and less overlap index information. Finally, the index system of soil and water conservation effect was formed by 8 ecological effect indices, 7 economic effect indices and 1 social effect index. The top three indices of ecological effects on soil and water conservation in rocky desertification region are area of forest and grass measures (11.21%), effective area of water storage measures (11.10%) and effective thickness of soil layer (6.28%), respectively. The top three indices of economic effects are the yield of fruit products (15.11%), grain production (14.95%) and total output value of the third industry (14.74%), respectively. However, the urbanization level in social effect index is a negative index, which shows that the higher level the urbanization is, the more serious the impact of human activities on degree of rocky desertification is, and the more difficult to control the soil and water loss. The final index system of this study provides a necessary technical support for further discussion on the compensation mechanism of ecological effects, and also gives a scientific basis for optimizing the water and soil conservation work in Guangxi rocky desertification region.