Functional groups in the molecule play an important role in the molecular organization process. To reveal the influence of functional groups on the self-assembly at interface, herein, the self-assembly structures of three liquid crystal molecules, which only differ in the functional groups, are explicitly characterized by using scanning tunneling microscopy (STM). The high-resolution STM images demonstrate the difference between the supramolecular assembly structures of three liquid crystal molecules, which attribute to the hydrogen bonding interaction and π-π stacking interaction between different functional groups. The density functional theory (DFT) results also confirm the influence of these functional groups on the self-assemblies. The effort on the self-assembly of liquid crystal molecules at interface could enhance the understanding of the supramolecular assembly mechanism and benefit the further application of liquid crystals.