The cyclic peptides can self-assemble into β-sheet like antiparallel tubular ensembles through intermolecular hydrogen-bonding interaction. Under the self-assembling effects of the dimer subunits, various aggregate properties may alter with the change of the structure. The relationship between the property and structure of ensembles is extremely important for designing new nanostructures. Molecular mechanics (MM) and molecular dynamics (MD) were employed to investigate the structure and property of single dimer and dimer-ensemble from cyclo-[D-Phe-(1R, 3S)-γ-Acc]3. Results reveal that the single dimer cannot adsorb CHCl3 molecule into its cavity, while the two-dimer ensemble can do. It suggests that the self-assembled cyclic peptide nanotube from the dimer-ensemble may act as the transport channel of CHCl3 molecules.