Using carbon nanotubes (CNTs) as building blocks in silicon-based electronics requires good electric contacts between the tubes and other devices. Recent experimental and theoretical works have shown that irradiation can be used to modify both the structure and the electrical properties of nanotubes, and also to create new covalent bonds to different nanotube structures. In this study, we have used atomistic computer simulations with analytical, empirically fitted interaction models, to examine the possibility to enhance binding between a CNT and a silicon substrate with C, Si and Ne ion irradiation. Low irradiation doses (<2.8×10¹⁴ ions/cm²) and energies (0.2–2.0 keV) were used, to ensure that the irradiated nanotube will not be destroyed. Our results indicate, that ion irradiation can be used to create new covalent bonds, and also to increase the binding energy between these structures, when the irradiation doses and energies are carefully chosen. We found that a typical number of created new covalent C–Si bonds is 0.5–0.9 (10¹⁴ ions/cm²)⁻¹, and a typical increase in the binding energy between the structures is 100–400% for moderate irradiation doses.