Fe75Zr25/Cu64Zr36 amorphous multilayers were prepared by magnetron sputtering. Atom probe tomography was employed to analyze the atomic inter-diffusion at the interface of the multilayers before and after annealing (573 K, 60 min). An unexpected enhanced inter-diffusion of the immiscible elements Fe and Cu was detected at the interface of the multilayers. As the inter-diffusion in amorphous multilayers is much faster than that in the crystalline counterparts, this process may open a way to manipulate or create amorphous multilayers with new properties. This idea agrees with the observation of the variation of magnetic properties of Fe75Zr25/Cu64Zr36 amorphous multilayers.