This paper studied the effect of long term concrete creeping behavior of pre-stressed concrete bridge on the vibration of track structure and ridding comfort of high speed rail. Track irregularity can be induced by creeping of pre-stressed concrete bridges. The finite element analysis software ANSYS was used in this paper to calculate the deflection of viaduct by concrete creeping. To consider the pre-stressed effect, we build a five-span concrete bridge model with pre-stressed tendons and calculate the creep coefficient according to the code of CEB-FIP 1995. Vertical deflections by concrete creeping in 20 years were presented in several period. A 4-carbody train passing through deflected bridge in different creeping time was taken into consideration. We use the finite element analysis software, LS-dyna, to perform dynamic analysis. The total accelerations on the car were calculated and the riding comfort was evaluated by ISO 2631-4(2005).