Different reactivity of ions has been implanted into Zr-Cu metallic glass to obtain nano-structured surface with controlled elasticity. The penetration of glass forming element of Ni+ into crystalline Zr-Cu stabilizes glassy phase to induce crystalline-amorphous (c-a) transition during implantation process. In the meanwhile, penetration of N+ into glassy matrix induces precipitation of (Zr, Cu)N at the mean penetration depth of N. Critical N concentration for nitride formation is estimated to be (Zr,Cu)-20at%N, which also suggests existing of N solid solution of glassy phase. Inert element of Ar+ yields dispersion of nano-voids among glassy matrix. Nano-indentation tests reveal that Young’s modulus of ion implanted glassy film dramatically changes with respect to the induced nano-structure, to decrease 0.4 times for Ar+, to increase 1.3 times for N+ as comparison with that for as-deposited state.