In this study, molecular simulation was used to explore the structural characteristics and transport performances of cyclic peptide nanotubes (CPNTs). A molecular dynamics (MD) technique was used to construct four different molecular models of nanotubes: an octamer prototypical cyclic peptide (8CP); and, three cyclic peptides modified by replacing one or two L-Lysine or L-Leucine groups with an aromatic amino acid, 3-amino-2-methylbenzoic acid (gamma-Mba-OH). MD simulation was used to explain how the hydrophobic modification of functional group affects the structure, channel volume, interior affinity, and transportation behavior of water in CPNTs. The Monte Carlo (MC) method was adopted to investigate the sorption behaviors in these four types of CPNTs. The internal diameter, channel morphology, and volume analyses indicated that modified functional groups disrupted the symmetry of cyclic peptides and changed the structural characteristics of the nanotubes. The hydrogen bond distribution and interaction energy analyses suggested that the modified gamma-Mba-OH functional groups reduced the interior affinity between water molecules and nanotubes, which led to hydrophobic properties. The adsorption analysis revealed that a greater number of modified functional groups in CPNTs resulted in a lower affinity for water molecules, which lowered the adsorption amount in low-pressure regions. The modified gamma-Mba-OH functional groups lowered the attractive forces and enlarged the channel volume, which was reflected in the diffusion calculation that showed improvements in water diffusivity in most cases. The results of the structure and water transport properties of CPNTs, as shown by the MD technic and MC methods, provided useful information that would have been difficult to obtain in an actual experiment. The simulation techniques can assist in the analysis of nanotube structural properties and in the transport behavior of the molecules in CPNTs.