A fundamental and systematic study on the fabrication of a supramolecularly assembled nanostructure of an organic ligand-capped CdS nanocrystal (NC) and multiple heptamine beta-cyclodextrin ((NH2)(7)beta CD) molecules in aqueous solution has been here reported. The functionalization process of presynthesized hydrophobic CdS NCs by means of (NH2)(7)beta CD has been extensively investigated by using different spectroscopic and structural techniques, as a function of different experimental parameters, such as the composition and the concentration of CD, the concentration of CdS NCs, the nature of the NC surface capping ligand (oleic acid and octylamine), and the organic solvent. The formation of a complex based on the direct coordination of the (NH2)(7)beta CD amine groups at the NC surface has been demonstrated and found responsible for the CdS NC phase transfer process. The amine functional group in (NH2)(7)beta CD and the appropriate combination of pristine capping agent coordinating the NC surface and a suitable solvent have been found decisive for the success of the CdS NC phase transfer process. Furthermore, a layer-by-layer assembly experiment has indicated that the obtained (NH2)(7)beta CD functionalized CdS NCs are still able to perform the host guest chemistry. Thus, they offer a model of a nanoparticle-based material with molecular receptors, useful for bio applications.