(1) Background: Currently, nanomaterials have been broadly used in various applications including engineering, medicine and biology. One of the carbon allotropes such as carbon nanotubes (CNTs) implemented for fabrication of nanocomposite materials due to the hypersensitivity. The combined design of nanomaterial with chitosan (CS) and CNT expands the field of exploitation from biosensing and tissue engineering to water desalination. Therefore, the penetration of CS into CNT provides a valuable insight into the interactions between CS and CNT. (2) Methods: We performed molecular dynamics simulations, applying the umbrella sampling method, in order to calculate the potential mean force between CS and CNT. (3) Results: The estimated penetration free energies showed that CS is favorable to the penetration into CNT cavities. However, the penetration nature differs depending on the CNT’s architecture. (4) Conclusions: Our finding revealed the CS penetration process into CNT with nanoscale precision. The investigation results assist in a better understanding of the nanocomposite materials based on CS-CNT.