Quercetin, one of the most abundant flavonoid in the daily diet, was found to reversibly inhibit the generation of uric acid and superoxide radicals (O2−)catalyzed by xanthine oxidase (XOD) in a mixed-type manner with IC50 values of (2.74±0.04)×10−6 and (2.90±0.03)×10−6molL−1, respectively, and the inhibition of quercetin on O2− generation may be ascribed to the reduced form of XOD by a ping-pong mechanism. XOD had one high affinity binding site for quercetin with a binding constant of 4.28×104Lmol−1 at 298K, and the binding process was predominately driven by van der Waals forces and hydrogen bonds on account of the negative enthalpy and entropy changes. Moreover, molecular docking confirmed that the binding site for quercetin located in the isoalloxazine ring of the flavin adenine dinucleotide (FAD) domain of XOD, then the diffusion of O2− out of the FAD site was blocked in favor of another electron transferred from FADH2 to O2− to form hydrogen peroxide (H2O2). This study may clarify the role of quercetin on inhibiting XOD catalysis and provide a potential nutritional supplement for preventing gout and peroxidative damage.