Due to significance of the engineering system for flood control and the multi-dimensional synthesis of the risk evaluation issue that the paper selects typical risk indexes to classify risk degree of flood-control engineering. Under global view of system that the variable fuzzy sets method is presented to set up comprehensive evaluation model for flood-control engineering system (FCES). The method can scientifically and reasonably determine membership degrees and relative membership functions of disquisitive indexes at level interval that relating to engineering, also it can fully use one’s experience and knowledge, qualitative and quantitative information of index system to obtain weights of indexes for operating comprehensive risk evaluation for FCES. The numerical example shows that the proposed method is feasible and effective, and the evaluation results are reasonable.