In this study, the transport performance of water molecules and the ion-rejection ability of cyclic peptide nanotubes (CPNTs) were examined on a molecular level via a simulation of forward osmosis (FO) filtration phenomena. A FO filtration model and three types of CPNTs, 8CP, Mba-8CP, and 4Mba-8CP (with different levels of modification by hydrophobic functional groups), were constructed via molecular dynamics (MD). MD simulation was adopted to explain the diversity transport mechanism between different types of CPNTs, and to analyze how hydrophobic modified functional groups affect the FO filtration process. The hydration structures of cations and anions were validated via radial distribution function (RDF) and hydration analysis. The interaction energy of van der Waals (vdW) and coulombic energies at the interface between water molecules and the first cyclic peptide cage suggested that hydrophobic modified functional groups reduced the interior affinity between water molecules and nanotubes, which made it difficult for water molecules to enter a nanotube. During FO filtration calculation, the alteration in the number of water molecules in each region of saltwater, pure water and membrane was traced and recorded. The osmotic pressure was considered as the driving force for concentration driven FO process which was calculated via the Van't Hoff equation in this work. By combining the above results, water permeabilities of the three types of CPNTs could be directly calculated and compared. The results of the water permeabilities agreed well with the interaction energy analysis. Finally, the hydration structure of cations within a nanotube was used to directly study the ion rejection mechanism of CPNTs. Three types of CPNTs showed high selectively between water molecules and ions. The partial charge distribution of a cyclic peptide cage illustrated how cations are trapped within nanotubes. A microscopic view of this information was informative in the analysis of nanotube properties and in the application of CPNTs to the filtration process.