The complex methods of transmission electron microscopy, energy dispersive X-ray analysis, and X-ray photoelectron spectroscopy were used to investigate the changes in the morphology, phase composition, and electronic structure of the composite SnO2−x/nitrogen-doped multiwalled carbon nanotubes (SnO2−x/N-MWCNTs) irradiated with the pulsed ion beam of nanosecond duration. The irradiation of the composite SnO2−x/N-MWCNTs leads to the formation of nanoparticles with the core–shell structure on the surface of CNTs with a sharp interfacial boundary. It has been established that the “core” is a metal tin (Sn0) with a typical size of 5–35nm, and the “shell” is a thin amorphous layer (2–6nm) consisting of nonstoichiometric tin oxide with a low oxygen content. The “core–shell” structure SnSnOx is formed due to the process of heating and evaporation of SnO2−x under the effect of the ion beam, followed by vapor deposition on the surface of carbon nanotubes.