A moving wheel-rail interaction element incorporating rail irregularity is derived, and the finite element equations of motion for the train-rail-bridge interaction system are established. Then, the long-term creep deformation increment of an actual pre-stressed concrete girder is predicted based on the modified creep-prediction model, and the real rail creep irregularity of a multi-span simply supported bridge is analyzed in consideration of the rail smoothing effect. Finally, the influence of the rail smoothing effect on the dynamic response is discussed by a numerical example. Also, the influences of the creep irregularities at different periods are investigated, and the effects of a control method of delaying the track-laying time for about half year for mitigating the creep irregularity are studied. The results indicate that the periodic creep irregularity can excite significantly both the natural vibration and the forced vibration for the vehicle, and leads to the sharp impact at the beam end, thereby increasing dramatically the car body acceleration and the contact force. The continuous rail structure can smooth obviously the turning angle of the creep deformation and the impact at the beam end, and should be taken into account for a more accurate analysis. Moreover, the control method has distinct control effects, especially for the car body acceleration as well as the bridge acceleration.