Studying two-dimensional (2D) and three-dimensional (3D) crystallization in tandem is a powerful way to acquire a deep understanding of molecular self-assembly. X-ray crystallography results indicate that N-[6-(fluoren-9-ylideneamino)hexyl]fluoren-9-imine (C1), N-[12-(fluoren-9-ylideneamino)dodecyl]fluoren-9-imine (C2), and co-crystal of naphthalene-1,5-diamine and 9-fluorenone (C3) are single-, poly- and co-crystals, respectively. Furthermore, the self-assembled structures of these three kinds of crystals (C1, C2 and C3) at the 1-phenyloctane/HOPG interface are investigated using scanning tunneling microscopy under ambient conditions. The C1 molecule, with a short chain, is lying flat on the substrate with a close packing phase, which is the same in its 3D crystal structure. The C2 molecule, bearing a longer chain, forms two types of linear structures, which are stable enough to endure continuous tip scanning. In Type I, the C2 molecules lie flat on the substrate to form a linear zigzag pattern, while in Type II one of the fluorene cores in each C2 molecule adopts an edge-on arrangement and interlocks with the adjacent fluorene core in one lamella. In the co-crystal C3, naphthalene-1,5-diamine and 9-fluorenone arrange perpendicular to the HOPG surface in a herringbone pattern via hydrogen bonds and π–π interactions. The lying or standing orientation of the three kinds of crystals show that the functional groups tethered to the middle spacer can modulate the motifs of self-assembly in the 2D and 3D crystallization. Furthermore, it also highlights that physical adsorption on the HOPG surface is not only controlled by the adsorbate–substrate interactions but also by the size and shape of the adsorbates.