Study of proton beam induced welding of multiwall carbon nanotubes (MWCNTs) with ZnO nanowires (NWs) has been carried out by proton (H +) beam irradiation. The samples were irradiated by 70-keV proton (H +) ion beams at different substrate temperatures. The irradiation-induced defects in CNTs and ZnO NWs were greatly reduced at elevated temperature. The crystalline structure of ZnO NWs and MWCNTs were found to remain stable after the irradiation at 700 K. As a preparation step, a coupling of two parallel ZnO NWs with irradiation has also been demonstrated. The welding mechanisms of MWCNTs and ZnO NWs were also been suggested. These two welding processes between same and distinct nanostructures to form homo- and hetero-junctions have provided an opportunity to mass produce interconnecting one-dimensional structures used for the manufacturing of future nanowire-based electronic circuits and devices.