Nanoporous copper (NPC) is the potential affordable surface-enhanced Raman scattering (SERS) substrate in practical use, although restricted by a relatively small enhancement factor. In this report, Cu ion irradiation is applied to effectively increase the enhancement factor of NPC. Two levels of surface roughness in NPC after ion irradiation are proposed to account for the improved SERS effect by careful characterization of microstructures. This study provides a new strategy to acquire a higher Raman enhancement factor in NPC, which perhaps can be extended to other SERS substrate systems.