The device yield of molecular junctions has become a major issue for the practical application of molecular electronics based on a crossbar system of a metal-molecule-metal (MMM) junction. As the thickness of self-assembled monolayers (SAMs) is typically 1-2 nm, it is difficult to avoid electrical shorts due to the penetration of top metal particles into the SAMs. A simple and effective strategy for the creation of a reliable molecular junction using a thickness-controlled bilayer with a bifunctional heterostructure is presented. In the MMM device, the Au adlayer on the molecular layer is spontaneously formed with deposition of the top Au metals and the sandwiched molecular layer maintains the quality of the SAMs. This method greatly reduces electrical shorts by preventing the diffusion of the top metal electrode and offsetting the surface roughness of the bottom metal electrode, resulting in a device yield of more than 90%.