To investigate the effect of flexible car body vibration on the dynamic responses of vehicle-bridge system, the dynamic analysis model of a vehicle with flexible car body moving over multi-span bridges is established, and the dynamic responses of this system is computed by Newmark-β method. In this model, the car body is regarded as an Euler beam with both ends free, and the bogie and wheel set are regarded as rigid. The multi-span bridges are regarded as a series of simple bridges and the vibration of the bridges are determined by modal superposition method, and the vehicle and bridge are linked by the wheel-rail corresponding assumption. A series of irregularities are chosen as the system excitation, and the resonance and cancellation of the flexible car body are analyzed. The calculation results show that the vibration of the flexible car body has some effect on the car body dynamic responses, which shows little feedback to the bridge vibration. The flexible resonances of the car body may result in significant amplification of the dynamic responses of the car body, and the flexible resonant speeds are determined by the bogie spacing and the car body flexible natural frequencies. Due to the wheelbase filtering effect, that is when the cancellation of the flexible car body vibration occur, the dynamic responses of the car body can be effectively suppressed.