The flow-induced vibration characteristic of the U-section rubber outer windshield structure of high-speed train is the key factor to limit its high-speed movement. Accurate and effective flow-induced vibration analysis of windshield structures is an important topic. In this paper, a hybrid modeling method for the analysis of flow-induced vibration of windshield structure is innovatively proposed for the U-section rubber windshield system of high-speed train. The method uses the external aerodynamic load obtained by aerodynamic simulation as the input condition of the flow-induced vibration model, and maps the aerodynamic load to the structural dynamics model characterized by the modal test data of the windshield structure. The flow-induced vibration model is established by means of modal superposition method and the time-domain response is effectively integrated by Runge Kutta method with variable step size. The results show that this method can effectively simulate the flow induced vibration of the wind baffle structure, and the real-time relationship between the aerodynamic load and the modal characteristics of the structure and the response of displacement and velocity can be obtained. On this basis, the comprehensive dynamic performance of the windshield system of high-speed trains at 400 km/h under external aerodynamic load is studied, that is, the force, displacement and velocity variation rules of the flexible structure are examined. It is determined that the displacement and velocity response curve of the measuring point near the lower side of the U-section rubber outer windshield is significantly higher than that of other parts. Moreover, the contribution of the first mode to the dynamic response of the structure is very obvious. This method provides an efficient calculation method for analyzing the flow-induced vibration characteristics of complex flexible structures.