To establish an evaluation method for the ecological benefits of rocky desertification control in karst areas, data reference was provided for the benefits of the national comprehensive control project of rocky desertification. This article analyzed the spatiotemporal variation characteristics of soil conservation, water yield, and net primary productivity (NPP) of southwestern China using GIS spatial analysis technology and INVEST Model, the trade-offs and synergistic relationship between ecosystem services and its influencing factors were discussed. The results showed that: (1) During the 15 years, the average value of ecosystem services showed an increasing trend. NPP, water yield, and soil conservation were increased by 43.04 gC/m(2), 4.37 mm, and 15.4 t center dot ha(-1), respectively. (2) There was a synergistic relationship between NPP and soil conservation. Increased NPP could improve soil erosion, while water yield exhibited trade-off relationship with NPP and soil conservation. (3) Over the past 15 years, the average comprehensive score of the ecological condition in the study area has increased from 0.30 to 0.31, meanwhile the ecological situation of the study area is gradually improved. (4) Through the analysis of hotspots, we found that more than half of the regions had no hotspots for ecosystem services, meanwhile this region was mainly karst area. Through this study, the trade-offs and synergies between ecosystem services were understood. The ecological benefits of rocky desertification control were evaluated based on the background of ecosystem services, which also provided a reference for the subsequent research on rocky desertification control.