The key to the system identification is the structure identification of the model, which includes assuming its prior structure and determining structure parameter. The structure identification of the model on the linear system is virtually to determine the structure parameter of the model. In this paper, the fighter movement mathematical models are taken as the research object；a new method on the structure identification of the model is introduced，which is based on Bayes theory and suitable for the linear system. Finally, an actual example of engineering application is given.