The developed vertical coupling model of Vehicle-Track-Subgrade which considered subgrade layer vibration is presented. The equations of motion for the ballast, top and bottom subgrade layers are presented in detail. Through inputting different coefficients, the dynamic response of track-subgrade system in a seasonal frozen region in different seasons is obtained by the developed model and the uneven freeze-thaw action of subgrade soil is presented in this model. The effect of subgrade inhomogeneity induced by uneven freeze-thaw on the dynamic response of track-subgrade system was studied and the conclusions are as follows. The force at the interface of ballast and top subgrade layer and the deformation of ballast induced by a passing train changed sharply at the stiffness mutation zone. The force and deformation decreased with increasing stiffness ratio with the same amplitude of irregularities as the excitation source. The force and deformation were larger with larger amplitudes of irregularities. There was an obvious effect of uneven deformation and stiffness of subgrade on the dynamic response of track-subgrade system. The developed vertical coupling model of Vehicle-Track-Subgrade which considered subgrade layer vibration is presented. The equations of motion for the ballast, top and bottom subgrade layers are presented in detail. Through inputting different coefficients, the dynamic response of track-subgrade system in a seasonal frozen region in different seasons is obtained by the developed model and the uneven freeze-thaw action of subgrade soil is presented in this model. The effect of subgrade in homogeneity induced by uneven freeze-thaw on the dynamic response of track-subgrade system was studied and the figures are as follows. The force at the interface of ballast and top subgrade layer and the deformation of ballast induced by a passing train changed sharply at the stiffness mutation zone. The force and deformation decreased with increasing stiffness ratio with the same amplitude of irregularities as the excitation source. The force and deformation were with larger amplitudes of i rregularities. There was an obvious effect of uneven deformation and stiffness of subgrade on the dynamic response of track-subgrade system.