Carbon nanotubes (CNTs) are expected to play a pivotal role in future space device applications owing to their exceptional material properties. To ensure the reliability and safety of CNTs in such applications, meticulous assessment and understanding of their structural integrity under ions irradiation is imperative. In this study, the mechanisms of damage to 1–5 wall CNTs caused by the irradiation of He²⁺ ions in the 1–100 keV energy range were investigated by conducting molecular dynamics (MD) simulations. The mechanisms of damage induced by He²⁺ ion irradiation exhibited notable distinctions between single-walled carbon nanotubes (SWCNTs) and multi-walled carbon nanotubes (MWCNTs). SWCNTs easily conducted the kinetic energy of the He²⁺ irradiation out of the CNTs with cascade collisions, thereby reducing the damage they incurred, whereas the interlayer structure of the MWCNTs resulted in the irradiation energy being confined inside the tubes, leading to an increase in defects. The MD simulations revealed the irradiation swelling phenomenon of the MWCNTs in relation to the kinetic energy of irradiation and the cumulative fluence and indicated that swelling occurred simultaneously inward and outward along the radial direction of the CNTs. Irradiation-induced swelling was observed in experiments involving vertical array carbon nanotubes (VACNTs) irradiated with 540 keV He²⁺ ions. The results from scanning electron microscopy (SEM) and transmission electron microscopy (TEM) characterization, along with the Raman analysis, indicate that the damage observed in CNTs due to He²⁺ ion irradiation closely resembles the findings obtained through MD simulations. Both experimental and MD simulation studies demonstrated that increasing the dosage of He²⁺ ion irradiation increased the CNT defects, causing a transition from the ordered graphite structure to amorphous C. Additionally, the compressive mechanical properties and surface adhesion mechanics of the irradiated VACNTs were examined by performing nanoindentation experiments. The tensile mechanical properties of the irradiated CNTs were evaluated using MD simulations. The combined results indicated that high-energy, high-fluence ion irradiation degraded the mechanical properties of the CNTs. This study comprehensively investigated the mechanisms of damage to CNTs under He²⁺ ion irradiation and the subsequent impacts on the mechanical properties of the CNTs. The findings of this research provide essential insights for comprehending the irradiation responses of CNTs and for designing composite CNT materials with enhanced radiation resistance.