Karst waterlogging is a natural disaster that occurs frequently and it adversely affects the social and economic development of affected areas. An analysis of the causes of karst waterlogging with respect to climate and topography can serve as a foundation for disaster assessment and prevention. In this study, a karst waterlogging risk assessment indexing system was established. The system was based on a comprehensive analysis of risk factors, including the severity of the disaster and the vulnerability of the affected area. DeBao County in GuangXi was used as the study area. Nine risk indicators were chosen as evaluation indexes and combination weights were divided into subjective and objective weights based on the analytic hierarchy process (AHP) and entropy weight. A geographical information system (GIS) was applied to help with the calculations of the set pair analysis (SPA) and to pile up the layers of the evaluation indicators. Then, a risk rating map was drawn using GIS techniques. The results showed that the high risk locations were mainly distributed in the center of DeBao County; therefore, the map could be used as reference for the prevention and management of karst waterlogging risk.