In this study, ion beam treatment was investigated as a method for functionalizing the surfaces of multi-walled carbon nanotubes (MWCNTs) employed in the production of composites with titanium and tin oxides using magnetron sputtering. Preliminary ion irradiation of MWCNTs obtained a uniform distribution of metal oxides over their surfaces. According to the experimental results, interfacial adhesion in the composites was increased due to the interactions between metal oxides and oxygen-containing functional groups on the surfaces of the MWCNTs. Quantum chemical calculations demonstrated the possibility of M-O-C bonds (M = Ti, Sn) forming with the participation of C[dbnd]O groups fixed on the graphene plane near vacancy-type defects. The features of Ti–O–C and Sn–O–C bonds were investigated based on electron density difference analysis and the density of states of the outer electron shells.