In order to scientifically assess the social stability risk of water conservancy projects and to comprehensively identify and prevent the social stability risk, the risk assessment index system for social stability is designed from the perspective of internal and external risk sources. Meanwhile, GAHP is chosen as the assessment model. The aggregated judgment matrix is used to calculate the index weights. The multi-level FCE is chosen to determine the values of risk assessment. Finally, the case study of bank collapse emergency management project of Jiangsu Section of Yangtze River indicates that its social stability risk is low. Finally, some prevention and control measures for the sensitive risk factors are put forward.