Understanding the formation of crystalline polymorphs is of importance for various applications of materials science. Polymorphism of Schiff base derivatives has recently attracted considerable attention because of its influence on photochromic and thermochromic properties of their 3D crystals. The present investigation extends the study of Schiff base polymorphism to the molecular level by using a combination of scanning tunneling microscopy at the liquid/solid interface and molecular modeling. It is demonstrated that polymorphism of 4-(dodecyloxy)-N-(4-dodecylphenyl)-2-hydroxybenzaidimine (PHB), a Schiff base substituted by alkyl side chains, can occur in 2D crystals when PHB is adsorbed on a surface that is able to exchange charge with the molecule. In particular, on Au(111), PHB molecules self-organize not only into a columnar packing but also in dimer structures. Theoretical and experimental results demonstrate that the dimer-based structure observed on Au(111) originates from molecule/surface interactions, which in turn modify molecule/molecule interactions. The results highlight that the Au(1 11) substrate is far from being a passive part of the self-assembled system and plays a crucial role in the morphology of 2D polymorphs.