Once a high speed train enters a tunnel, compression waves are generated at the front section of the train, and they are propagated with very high velocity along the tunnel. Recently, most of tunnels have the vertical air-shafts and the tunnel entrance hood. Many studies have been reported on the hood effect on the propagation of micro pressure waves, whereas few studies have been discussed on the vertical air-shafts. Therefore, this study examines the effect of vertical air-shafts on the transient behavior of micro pressure waves in the tunnels. For grid systems made by ICEMCFD (ver. 13.0), the present study simulated numerically the fluid flows which are closely associated with the propagating pressure waves by using a commercial CFD code, i.e., ANSYS FLUENT (ver. 13.0). Under the real operating conditions of KTX, three different cases were simulated to investigate the effect of vertical air-shafts on the pressure waves. In particular, we used the well-known dynamic layering method in describing dynamic movement of the train. From the results, it is found that the existence of flared section causes rapid change of flow fields and different behaviors of pressure waves, which is substantially dependent on moving direction of train. In addition, a maximum pressure difference is estimated 137.9 kPa in the case without any of air-shafts, whereas it can be reduced by 49.1 % to 50 % for the cases with air-shafts.