In order to study the effect of the vertical stiffness of the isolation damping pad on the vibration and noise of a U-beam bridge structure, this study adopts the method of multi-body dynamics and finite element co-simulation to establish vehicle-track-bridge rigid-flexible coupling dynamics based on the Timoshenko beam model. The model is learned, and the theoretical calculation results are compared with those of previous studies to verify the effectiveness of the model. Based on this model, the vibration and noise responses of the bridge system under different vertical stiffnesses of the cushions were calculated. The results show that as the vertical stiffness of the isolation damping pad increases, the vibration response of the rail and track slab is reduced to varying degrees, but the vibration response of the bridge structure is amplified, as well as the vibration amplitude of the track structure and U-shaped bridge. The value first changes significantly, and then gradually changes more slowly; the increase in the vertical stiffness of the isolation cushion will increase the secondary noise of the bridge structure, so a smaller cushion stiffness should be selected to suppress the secondary structure of the U-beam bridge. A vertical stiffness that is too small may amplify structural noise in the low-frequency region within 40 Hz; integrated U-beam bridge system vibration and structural noise calculation results, considering the engineering cost, are used for isolation vibration reduction of elevated structures. A more appropriate vertical stiffness of the pad is 0.067 N/mm3.