A three-dimensional deformable finite element model of wheel-rail system is established. The vertical vibration natural frequencies are calculated by modal analysis. The improved central difference method by ABAQUS explicit nonlinear dynamics module is chosen to calculate the vertical vibration of wheel axle. Through the vibration measurement experiment ofLMAwheel by China Academy of Railway Sciences, the contact parameter is optimized and the model is modified. According to the nonlinear simulation results, the important influence of vertical track irregularity on the wheel set high-frequency vibration is discovered. The advantage frequencies through spectrum are close to the vertical vibration natural frequencies of seventh, eighth, ninth, and tenth mode. When the velocity is 350 km/h, system’s nonlinear dynamic characteristic is higher than the results at 200 km/h. The critical wavelength of vertical track irregularity on the wheel vertical vibration is about 0.8 m. In addition, a particular attention should be paid to one situation that the main dominant frequency amplitude is more than 50% of the acceleration amplitude even if the peak acceleration is low.