According to the regular pattern of development of agricultural drought and risk theory, from the perspective of crop losses caused by drought, analyzed the risk of hazard factor, environmental vulnerability of disaster and vulnerability of bearing body, established the agricultural drought risk assessment model, made cluster analysis combining GIS in natural breaks classification, developed regional agricultural drought risk regionalization. Selected Nanpanjiang basin in Yunnan as the study area, according to the standard classification of drought, made agricultural drought risk regionalization according to four levels, and analyzed the regionalization results. The research provides technical support for the development of disaster prevention and mitigation planning.