Flood control operation in a multi-reservoir system is a multi-criteria decision-making (MCDM) problem, in which the considered criteria are often correlated with each other. In this paper, we propose an MCDM model for reservoir flood control operation to deal with correlation among criteria. Considering the flood control safety of reservoirs and downstream protected regions, we establish the hierarchical structure of the criterion system. We use the principal component analysis method to eliminate the correlation, and transform the original criterion system into an independent comprehensive criterion system. The comprehensive decision matrix coupled with the weight vector obtained by the improved entropy weight method serves as the input to TOPSIS method, fuzzy optimum method, and fuzzy matter-element method, by which we determine the ranking order of the alternatives. We apply the proposed model to a cascade system of reservoirs at the Daduhe River basin in China. The results show that the dimensionality of the criterion system is reduced and the correlation among criteria is eliminated simultaneously, and the ranking order of the alternatives is reasonable. The proposed model provides an effective way to deal with correlation among criteria, and can be extended to wider applications in many other MCDM problems.