Factors that influence the security of navigation have the characteristics of dynamics, randomness, uncertainty and mutual influence, so the system of navigation security is a typical non-linear system. Due to the limitations of traditional mathematical methods solving the non-linear system, this article combines artificial neural network model and wavelet analysis to construct the wavelet neural network model for the navigation risk assessment, and puts forward the index system, weights calculation and algorithm with examples. Results shows that the wavelet neural network model for evaluating can be solved the defects such as subjective arbitrariness and the fuzzy of conclusions existing in traditional evaluation methods, and it can do better than the common artificial neural networks in fitting accuracy and convergence rate, so the application of wavelet neural network model has an important value.