The self-assembly behaviors of a benzothiadiazole-based liquid crystalline molecule (BT-C14) were investigated by scanning tunneling microscopy (STM). STM observations show the coexistence of three kinds of self-assembled patterns without apparent concentration dependence at the heptanoic acid/graphite interface, in which the molecules adopt two conformations due to different orientations of two flanked thiophene groups relative to cyano groups. BT-C14 molecules with one conformation form a linear structure by intermolecular CH∙∙∙NC hydrogen bonds and interchain van der Waals (vdWs) interactions. Meanwhile, the zigzag-like and separated-dimer patterns are observed, in which the molecules adopt another conformation. The CH∙∙∙NC hydrogen bonds and the S∙∙∙N chalcogen bonding in dimers, the dipolar interactions, along with the interchain vdWs interactions are the dominated forces to drive their structural formation. Density functional theory (DFT) approaches are utilized to determine the molecular conformations and the noncovalent interactions. Molecular dynamics (MD) calculations unravel that these three nanostructures have analogous interaction energies and molecular stacking densities, indicating that the coexistence is thermodynamically and kinetically favorable. This study not only instructs the design of liquid crystalline molecules but also provides a strategy for analyzing multi-configuration and multi-structure system in the self-assembly process.