After identification principle based on BP neural networks for nonlinear system was analysed, using simulation method, the influence of identification modeling with different BP neural networks model structures was studied. Through optimized to initial BP network model structure designed, the reasonable and optimized network structure was obtained, and simulation effects of identification modeling were compared with no optimized the BP neural network structure model. Simulation results show that the error of optimized BP neural network model is reduced, the generalization ability of network model is enhanced.