Finite-element analysis of the nanoindentation into Au/Cu and Cu/Au multilayers was performed to deduce their mechanical characteristics from nanoindentation response. Different bilayer thicknesses, numbers, and sequences were studied using the load–displacement curve, hardness, indentation, and the residual surface profile as well as the von Mises equivalent stress. The characteristics of the multilayers were found to be dispersed between the Au and Cu. Nevertheless, if the indentation depth is smaller than the uppermost individual layer thickness of the multilayers, the intrinsic properties can be obtained. Using the von Mises equivalent stress as a failure criterion, the results showed that thinner multilayers would induce a greater potential of shear banding deformation.