Using the methods of scanning electron microscopy (Scanning Electron Microscope – SEM) and X-ray photoelectron spectroscopy (XPS), changes in the atomic structure and chemical state of multi-walled carbon nanotubes (MWCNTs) due to the action of ion beams of argon and helium with different irradiation parameters were investigated. Based on the experimental XPS and XANES (X-ray absorption near edge structure) data, as well as theoretical data, changes in the density of electronic states near the Fermi level in MWCNTs after ion-beam action were analyzed. It is shown that the use of beams of argon and helium ions can be used for directional functionalization of MWCNTs and applications in the chemical and petrochemical industries.