The effect of layer thickness on the hardness of nanometallic material composites with both coherent and incoherent interfaces was investigated using nanoindentation. Then, atomistic simulations were performed to identify the critical deformation mechanisms and explain the macroscopic behavior of the materials under investigation. Nanocomposites of different individual layer thicknesses, ranging from 1–30 nm, were manufactured and tested in nanoindentation. The findings were compared to the stress–strain curves obtained by atomistic simulations. The results reveal the role of the individual layer thickness as the thicker structures exhibit somehow different behavior than the thinner ones. This difference is attributed to the motion of the dislocations inside the layers. However, in all cases the hybrid structure was the strongest, implying that a particular improvement to the mechanical properties of the coherent nanocomposites can be achieved by adding a body-centered cubic layer on top of a face-centered cubic bilayer.