The methods of ultraviolet and infrared spectroscopy and quantum chemical modeling have been used to evaluate the parameters of the formation of a supramolecular inclusion complex between the flavonoid quercetin and the hydroxypropyl-β-cyclodextrin molecular container. The solubility of quercetin in water has been shown to increase by a factor of more than 50 when included in a supramolecular complex with 16 mM hydroxypropyl-β-cyclodextrin. It has been demonstrated that bioavailability of quercetin is improved after encapsulation with hydroxypropyl-β-cyclodextrin. The association constant for the inclusion complex of quercetin and hydroxypropyl-β-cyclodextrin (1 : 1) has been evaluated by the Higuchi-Connors method to be 3275 ± 448 М–1. The formation of the inclusion complex results in considerable changes in the vibrational spectra of components compared to the spectrum of the physical mixture of quercetin and hydroxypropyl-β-cyclodextrin. This difference can be explained by structural changes of the components due to hydrogen bond formation. The molecular modeling of the inclusion complex has shown that the geometry and properties of the components change after encapsulation of quercetin molecule (“guest”) inside the cavity of β-cyclodextrins (“host”). The torsion angles between the rings of the planar quercetin molecule in the complexes with β-cyclodextrin and hydroxypropyl-β-cyclodextrin have been evaluated to be 149.5° and 138.7°, respectively.