The assembly behaviors of two low-symmetric carboxylic acid molecules (CTTA and BCBDA) containing naphthalene rings on graphite surfaces have been investigated using scanning tunneling microscopy (STM). The transformation of nanostructures induced by the second components (EDA and PEBP-C4) have been also examined. Both CTTA and BCBDA molecules self-assemble at the 1-heptanoic acid (HA)/HOPG interface, forming porous network structures. The dimer represents the most elementary building unit due to the formation of double hydrogen bonds. Moreover, the flipping of the naphthalene ring results in the isomerization of the BCBDA molecule. The introduction of the carboxylic acid derivative EDA disrupt the dimer, which subsequently undergoes a structural conformation to form a novel porous structure. Furthermore, upon the addition of the pyridine derivative PEBP-C4, N–H⋯O hydrogen bonds are the dominant forces driving the three co-assembled structures. We have also conducted density functional theory (DFT) calculations to determine the molecular conformation and analyze the mechanisms underlying the formation of nanostructures.