Hybrid structures made of metal nanoparticles with liquid crystalline coating attract considerable attention due to their conspicuous self-assembly and potential synergistic properties. Here we report on a new structural parameter that can be used to control the formation of hybrid gold nanoparticles superlattice. A series of Au nanoclusters covered with mixed monolayers of alkyl and liquid-crystalline ligands were obtained. For the first time in such systems the lengths of both alkyl ligands and mercapto-functionalized alkyl spacers of the promesogenic molecules were varied. The physicochemical properties of the obtained materials were investigated by different instrumental techniques, such as X-ray photoelectron spectroscopy (XPS), small-angle X-ray diffraction (SAXRD), and transmission electron microscopy (TEM). Interestingly, the applied variations of the grafting layer composition enabled the formation of ID (lamellar) and 3D long-range ordered structures with systematically changing thermal stability range. Such behavior is explained based on the structural parameters of the hybrid nanoparticles, namely the separation of the cores and ligand flexibility. This work gives some new insights into the nanoparticle self-assembly subject and points out the critical parameters controlling the degree of order within the self-assembled superstructures.