The self-assembly of heterogeneous bilayers on Au substrates was investigated using atomic force microscopy (AFM), X-ray photoelectron spectroscopy (XPS), and infrared reflection absorption spectroscopy (IRAS). The formation of a well-defined bilayer including different types of functional groups would be one of the desired goals to create varying surface functionalities. In this study, we examined the assembly of a hydrogen-bonded molecular layer to another functional alkanethiolate self-assembled monolayer (SAM) on the Au(111) surface. The chemical properties and bond strength of the hydrogen bonds at the interlayer differ from those of the Au-S bonds at the anchor of thiolate SAMs, therefore the adsorbed molecules are expected to form a stratified bilayer. In this study, on one hand, we revealed that imidazole-terminated alkanethiolate SAMs (Im-SAMs) have an atomically smooth topography but chemically inhomogeneous Au-S anchors, rather incomplete than n-alkanethiolate SAMs, on the Au(111) surface. On the other hand, we confirmed the self-assembly of the heterogeneous bilayers including Im-SAMs on the Au(111) surface, even in a mixed solution containing two types of molecules. These results show that the self-assembly of the bilayer stratified by H bonds and Au-S bonds is flexible and adaptable.