With the development of the railway network in a harsh environment, the additional bridge deformations accumulated over time may endanger high-speed trains passing through a bridge, since the bridge deformation directly affect the geometry of the track on the bridge, thus affecting the dynamic responses of the train. This paper investigates the effects of different types of bridge deformation on the dynamic responses of the high-speed train passing through a deformed bridge. First, a finite element model is established for a high-speed railway bridge to study the dynamic responses of vehicle-track-bridge system under bridge deformations. Then, the rail deformation caused by bridge deformation is calculated using a bridge-track deformation mapping model, and used as the excitation to the vehicle-track-bridge system to study the influence of bridge deformations on the dynamic responses of the train. Results show that the vertical bridge deformations mainly affect the vertical vehicle dynamic indices, and have negligible effect on the lateral dynamic indices. The additional bridge deformation generates an additional low-frequency excitation to the train. The bridge deformations mainly affect the dynamic responses at specific characteristic frequencies, which are independent on the magnitude of the deformation. The frequencies for bridge deformations are magnified at about 1 Hz, indicating that the additional bridge deformation may aggravate the vertical vibration of the train.