Since the advent of graphene ushered the era of two-dimensional materials, many forms of hydrogenated graphene have been reported, exhibiting diverse properties ranging from a tunable band gap to ferromagnetic ordering. Patterned hydrogenated graphene with micron-scale patterns has been fabricated by lithographic means. Here we report successful millimeter-scale synthesis of an intrinsically honeycomb patterned form of hydrogenated graphene on Ru(0001) by epitaxial growth followed by hydrogenation. Combining scanning tunneling microscopy observations with density-functional-theory (DFT) calculations, we reveal that an atomic-hydrogen layer intercalates between graphene and Ru(0001). The result is a hydrogen honeycomb structure that serves as a template for the final hydrogenation, which converts the graphene into graphane only over the template, yielding honeycomb-patterned hydrogenated graphene (HPHG). In effect, HPHG is a form of patterned graphane. DFT calculations find that the unhydrogenated graphene regions embedded in the patterned graphane exhibit spin-polarized edge states. This type of growth mechanism provides new pathways for the fabrication of intrinsically patterned graphene-based materials.