Two-dimensional self-assembled structures formed by diketopyrrolopyrrole Pigment Red 254 (3,6-bis(4-chlorophenyl)-2,5-dihydropyrrolo[3,4-c]pyrrole-1,4-dione) and its alkyl-derivatives at the liquid-HOPG interface were investigated by scanning tunneling microscope (STM). Pigment Red 254 is found to form two different surface structures (crystal-like structure and solvated crystal-like structure). Furthermore, in order to investigate the effect of hydrogen bonding, alkyl-derivatized Pigment Red 254 (PR-2Cn, n: alkyl chain length) were synthesized, and their self-assembled structures were analyzed. We found that surface structures of PR-2Cn varied depending on the intermolecular and molecule?substrate van der Waals interactions arising from the n-alkyl chains introduced instead of hydrogen bonding. Shorter alkyl chains of PR-2C10 resulted in the formation of multi domains. On the other hand, PR-2C12, PR-2C14, and PR-2C16 molecules that have longer alkyl chains formed stable single domain structures.