The paper introduces fuzzy neural network into the selection of medical institutions in subway station emergency in view of some negatives of previous evaluation approaches. It also makes comprehensive analysis about affecting factors of subway station incident, and constructs the evaluation index system, and then proposes a new evaluation approach. This approach is a fuzzy neural network. The parameters accident factors, medical institutions' conditions and external environment are trained firstly.Then to construct a fuzzy neural network evaluation model and thereby derive the evaluating value of the selection of medical institutions in subway station emergency. Experimental results show that this method is effective, feasible and highly accurate.