The fate of high velocity clouds (HVCs) will affect the evolution of the Milky Way. If currently observed HVCs survived the interaction with the halo gas and reached the Galactic disk eventually, HVCs could provide fuel for the star formation in the disk. For this reason, the collision of HVCs with the Galactic disk has been extensively studied via numerical simulations. Recently, an idea that some HVCs are accompanied by dark matter has been suggested based upon the scenario that HVCs originated from the stripped gas of satellite galaxies which tend to have dark matter. Along the similar line of reasoning, it is worth investigating the effect of dark matter on the collision of HVCs with the Galactic disk. By using the FLASH hydrodynamics code, we simulate this scenario and search for proper parameters of dark matter and baryonic matter that can explain the currently available observations such as the Smith Cloud.