With the frequent extreme rainstorm and flood events at present, it is necessary to carry out flood control transformation of substation in operation to avoid its damage by flood. By identifying and evaluating risks and taking corresponding pre-control measures, the risk of substation suffering from flooding can be reduced to the greatest extent. This paper presents a method for predicting substation flood control risk. Firstly, the finite element method (FEM) is used to preprocess the historical data of substation flood control. Secondly, the improved neural network model is constructed, and part of the data is used to complete the model training. Finally, the actual substation data verification shows that the accuracy of the model is higher than that of the traditional neural network model, which is a simple and effective method.