Railway transportation vehicles are developing towards highspeed and light weight. The vehicle body bears complex alternating loads, which greatly increases the risk of fatigue fracture of the vehicle body structure. In order to explore the influence of vehicle body structure vibration on the safety of vehicle structure, ANSYS Workbench was used to simulate the vehicle body mode. Combined with the modal test data of the EMU body in the service environment, the firstorder diamond (8~9 Hz), firstorder vertical bend (12~13 Hz), firstorder transverse bend (15~16 Hz) and firstorder torsion (17~18 Hz) model frequencies were extracted, and the vehicle finite element model was compared and modified. The measured data of the measured load spectrum were processed by using the rain flow counting method, and the load spectrum rain flow counting matrix was obtained. Based on the modal analysis, the harmonic response analysis was carried out, and the frequency response functions in the above different modal frequency ranges were obtained. The nCode fatigue simulation software was used to simulate the fatigue strength of the vehicle body, and the fatigue damage of the vehicle body in different frequency range was obtained. Miner linear cumulative fatigue damage theory was used to evaluate the fatigue damage of vehicle body. The results show that the frequency band near the firstorder diamondshaped mode (8~9 Hz) of the vehicle body causes the most damage to the vehicle body, and the damage location is near the intersection of the vehicle hook and bolsters.