The self-assembly of poly(di-n-butylsilane) (PDBS) and poly(di-n-hexylsilane) (PDHS) on the surfaces of amorphous carbon and highly oriented pyrolytic graphite (HOPG) have been investigated, respectively. The morphology and structures of these self-assembled thin films were studied by using atomic force microscopy, transmission electronic microscopy, and wide-angle X-ray diffraction. In the case of weak van der Waals interactions between absorbed molecules and substrate, i.e., on amorphous carbon, the self-assembly process was driven by absorbate-absorbate intermolecular interactions. For PDBS with weak absorbate-absorbate intermolecular interactions, the thin film showed organization lacking any measurable preferred orientation on the surface of amorphous carbon. While for PDHS with rigid backbone and strong intermolecular interactions, flat-on lamellae with silicon backbones perpendicular to the surface of amorphous carbon were formed. However, in the case of strong van der Waals interactions between absorbed molecules and substrate, i.e., on HOPG, the self-assembly process was tailored by the balance of absorbate-absorbate intermolecular interactions and molecule-substrate interactions. Both PDHS and PDBS thin films grew into edge-on lamellae on the surface of HOPG, which aligned according to a Mold symmetry. The silicon backbones of both polysilanes were parallel to the substrate surface and perpendicular to the long axis of edge-on lamellae. The results show that the structures of polysilane thin films can be controlled by varying the substrate.