The co-crystallization of quercetin (Qur) with a flexible molecule 4-(4-pyridinyldisulfanyl) pyridine (DPDS) in different solvents and conditions was investigated, yielded five multi-component crystalline phases and characterized with X-ray diffractions and thermal analysis. Although the crystal system of Qur-DPDS-MeOH and Qur-DPDS-Dioxane is the same, the desolvation results revealed that Qur-DPDS-MeOH transformed to Qur-DPDS when MeOH solvent molecules escape from the lattice, while Qur-DPDS-Dioxane transformed to Qur-DPDS-II through a similar process, which is same with Qur-DPDS-THF. These two cocrystal polymorphs Qur-DPDS and Qur-DPDS-II obey an enantiotropic relationship. Moreover, the formation of cocrystal solvates improves the packing efficiency of crystals. Crystal structure analysis showed that hydrogen bonds and conformations of the corresponding parent molecules play a major role in molecular assembly and crystal packing patterns, thus bring different physicochemical properties. Finally, the fluorescence spectra and quantum-chemical calculations were carried out to explore the difference in the optical-physical properties.