The cause of the high permeability in the flow of water in CNT (carbon nanotube)-based nanoscale materials remains to be elucidated. In this study, water impregnation simulations outside the VACNFs were performed using the molecular dynamics method to investigate the factors that cause high permeability by virtually changing the force field parameters. As a result, the permeability coefficient increased with increasing CNT content (VC) in the slip flow region. For the constant VC, the smaller the intermolecular force between water and CNTs, the higher the permeability coefficient. Because the intermolecular forces between water and CNTs are smaller than those between water and water, it may have an effect on the high permeability phenomenon. Furthermore, in the present VC change, the arrangement structure of the water molecules changed from a disordered structure, such as bulk flow, to a chain structure in the impregnation direction, which is also considered a factor for the increase in the permeability. Therefore, both the intermolecular forces between water and CNTs and structural change in the arrangement of water molecules were factors in the high permeability phenomenon.