Using persimmon tannin fraction (PT40), epicatechin-3-gallate-(4β→8, 2β→O→7)-epicatechin-3-gallate (A-type ECG dimer) and epigallocatechin-3-gallate (EGCG) as representatives of polyphenols and Chinese cobra snake venom phospholipase A2 (PLA2) as a model protein, different mathematical equations were compared to correct the inner filter effects produced by the fluorescence quenching of those polyphenols to PLA2 based on the gradient, linearity and intercept of Stern-Volmer regression equation. The results revealed that correction by the equation developed by Gauthier et al made a significant reduction in gradients. Besides, the linearity was clearly improved and the intercepts were closer to 1 after correction in all cases. The binding constant of PT40 and PLA2 declined by 60% and the inferred interaction forces were more convinced after correction by the above equation. Therefore, the equation developed by Gauthier et al was the most appropriate equation for correcting the inner filter effects when studying the interaction of polyphenols and protein using fluorescence quenching method.