On the basis of the disaster system theory and comprehensive analysis of flood risk factors, including the hazard of the disaster-inducing factors and disaster-breeding environment, as well as the vulnerability of the hazards-bearing bodies, the primary risk assessment index system of flood diversion district as well as its assessment standards were established. Then, a new model for comprehensive flood risk assessment was put forward in this paper based on set pair analysis (SPA) and variable fuzzy sets (VFS) theory, named set pair analysis-variable fuzzy sets model (SPA-VFS), which determines the relative membership degree function of VFS by using SPA method and has the advantages of intuitionist course, simple calculation and good generality application. Moreover, the analytic hierarchy process (AHP) was combined with trapezoidal fuzzy numbers to calculate the weights of assessment indices, thus the weights for flood hazard and flood vulnerability were determined by the fuzzy AHP procedure, respectively. Then SPA-VFS were applied to calculate the flood hazard grades and flood vulnerability grades with rank feature value equation and the confidence criterion, respectively. Under the natural disasters risk expression recommended by the Humanitarian Affairs Department of United Nations, flood risk grades were achieved from the flood hazard grades and flood vulnerability grades with risk grade classification matrix, where flood hazard, flood vulnerability and flood risk were all classified into five grades as very low, low, medium, high and very high. Consequently, integrated flood risk maps could be carried out for flood risk management and decision-making. Finally, SPA-VFS and fuzzy AHP were employed for comprehensive flood risk assessment of Jingjiang flood diversion district in China, and the computational results demonstrate that SPA-VFS is reasonable, reliable and applicable, thus has bright prospects of application for comprehensive flood risk assessment, and moreover has potential to be applicable to comprehensive risk assessment of other natural disasters with no much modification.