Proton-assisted self-assemblies of three linear dipyridyl polyaromatic molecules, namely, 4,4′-bipyridine, 1,4-di(4-pyridyl)-benzene, and 4,4′-di(4-pyridyl)biphenyl, at the heptanoic acid/highly oriented pyrolytic graphite interface were systematically studied with scanning tunneling microscopy. A major finding was that protons from strong acids could greatly accelerate the assembling processes of 4,4′-bipyridine and 1,4-di(4-pyridyl)benzene molecules and, in the case of 4,4′-di(4-pyridyl)biphenyl molecule, lead to structural transformation in the self-assembling process in analogy to the role of a catalyst in a catalytic process. The experimental results could be rationalized by a simple mechanism involving protonassisted formation of intermolecular hydrogen bonds, which provides new insights with regards to the self-assembling processes in solutions, especially under acidic bioenvironments.