In this study, some flavonoids were screened as potent xanthine oxidase (XO) inhibitors in vitro. Flavonoid 9 was demonstrated to exhibit the inhibitory activity through a ping-pong mechanism. Further structure-activity relationship revealed that different structural elements had greatly influenced the inhibition effect on XO and underlined the requirement of hydroxyl groups at C5 and C4' of flavonoid type I. Moreover, some bioactive flavonoids could efficiently quench the intrinsic fluorescence of XO by either static or static-dynamic mixed mechanism. The synchronous fluorescence, ANS-binding fluorescence, Fourier transform infrared spectra and circular dichroism suggested that active flavonoids could bind to the active center of XO, prevent the entrance of substrate, and induce the rearrangement and conformation change of its secondary structures, ultimately resulting in the significant inhibition effect. Additionally, molecular docking further confirmed these conclusions and highlighted the great importance of hydrophobic interactions and hydrogen bonds for the formation of stable complex conformation.