Carbon nanotubes (CNTs) are one of the possible building blocks for electronic devices in the transition phase from traditional silicon-based microelectronics towards the few-nanometer regime. Remaining problems in integrating CNTs to the existing technology is the low reactivity of the CNT walls which leads to low conductance between CNTs and the other components. Because recent studies have shown that ion irradiation can be used to modify both the electrical and structural properties of CNTs, we propose that it could also be possible to use ion irradiation with low energies to enhance the conductance of these connections. We have used classical molecular dynamics simulations with empirically fitted potentials to examine this possibility by irradiating a single-walled carbon nanotube (SWCNT) on a silicon substrate at room temperature. The nanotube was deposited over a trench created to the silicon substrate so that the nanotube was partly suspended. Low irradiation doses and low energies (0.2 keV − 1.2 keV) were used to ensure that the irradiated CNT will not be destroyed. The simulations were carried out for silicon, carbon and neon ions. Our simulations indicate that ion irradiation will increase the number of covalent bonds between the CNT and the Si substrate. When the irradiation dose and energies are low, the damage caused to the SWCNT atomic network can be tolerable when compared to the improvement in the conductance of the contact regions. Furthermore, as the CNTs have high ability to heal the irradiation-induced damage, it is possible that the irradiation will not have a significant negative effect to the conductivity of the CNT in a system of this type.