N-implantation has been conducted for Zr and Zr-Cu films to investigate the phase-separation sequence depending on the different formation enthalpy of nitrides, ZrN and Cu3N. The films of Zr and Zr-12at%Cu have been prepared by ion beam sputtering and respective films consist of hcp-Zr and nano-crystalline hcp-Zr(Cu). Penetration of N2+ with the beam energy of 60keV induced surface nitriding of Zr-Cu films with the thickness of 100 nm in depth. The XPS depth profiling shows the composition of (Zr, Cu)-47at%N in maximum with dose of 2.5×1017 ions/cm2. SAED pattern reveals the formation of Zr-rich nitride and Cu-rich bcc phases, which implying the phase separated nano-complex with increasing N concentration.