Carbon nanotubes (CNTs)-based devices and their applications have received more and more attention, and several biomolecules have been found to be encapsulated into the inner space of the CNTs spontaneously. In this work, the molecular dynamics simulations demonstrate that a collagen-like peptide with a hydrophobic center and hydrophilic surfaces could be inserted into CNTs spontaneously but slowly. Then the dynamic mechanism of the encapsulation process was investigated by a series of steered molecular dynamics simulations. The van der Waals interaction between the peptide and the carbon nanotubes was proved to be a positive factor for this insertion process, whereas the major resistance of this process is attributed to the repelling of the trapped water molecules and the breaking of the hydrogen-bond networks of water molecules around the peptide. Because of the synthetical effect of these interactions, there is an optimal tube size corresponding to effective encapsulation of the protein into the CNTs for a given kind of protein molecule.