Different thickness of amorphous/nanocrystalline multi-layered structure can be used to modulate the strength and ductility of the composite materials. In this work, molecular dynamics simulations were conducted to study the thickness effect of nanocrystalline layer on mechanical properties and deformation behavior of the Cu64Zr36/Cu multi-layer structure. The stress-strain relationship, local stress, local strain, and deformation mechanism are investigated. The results reveal that the change of thickness of the crystalline layer significantly affects the mechanical properties and deformation behavior. As the strain at the elastic region, the amorphous Cu64Zr36 layer dominates the mechanical behavior, leading the fact that Young's modulus, first yielding stress, and first yielding strain are close to that of Cu64Zr36 BMG. As the strain at the plastic region, the contribution of the crystalline layer on the mechanical behavior becomes more and more significant with increasing the thickness of the crystalline layer. For the thickness ratio (amorphous/crystalline) of 4, the shear band deformation of amorphous layer dominates the mechanical properties. For the thickness ratio is 1, the glide dislocation of the crystalline layer dominates the stress-strain behavior.