The creation of novel supramolecular architectures through self-assembly of simple organic semiconductor molecules is one of the most promising approaches for the design of microelectronic devices. Offering several attractive features for molecular self-assembly and the resultant nanomaterials (e.g., high charge mobility, thermal stability and monomer solubility), oligothiophene-bridged-silsesquioxanes and their analogs have received much attention in the past decade. Here we present a unique example of the synthesis of ordered, conjugated, organic/inorganic nanocomposites with improved thermal stability and electronic properties from preprogrammed molecular building blocks. The mechanism of the molecular self-assembly and the details of the molecular packing have been studied through Molecular Modeling and Simulation. We found that the major driving forces operating in the self-assembly process are the non-covalent intermolecular interactions including π-π stacking, hydrogen bonding, and van der Waals interactions. We also studied the effect of the structure of the molecular building block on the properties and morphology of the self-assembled nanomaterials. We demonstrate that by modifying the nature of the side chains and the conjugated backbone, the properties and morphology of the assembled nanomaterials can be manipulated.