The pit mud-like odor is an unpleasant odor in strong flavor Baijiu, and the addition of kafirin can reduce the pit mud-like odor in strong flavor Baijiu. In this study, the underlying mechanism of the effect of kafirin on reducing the pit mud-like odor was studied. 3-Methylindol and p-cresol were regarded as the key aroma compounds that caused pit mud-like odor in strong flavor Baijiu. The aroma profile analysis showed that the addition of kafirin significantly suppressed the pit mud-like off-odor, while did not significantly affect other flavors. Headspace solid-phase microextraction analysis verified that kafirin had a reduction effect on the volatility of 3-methylindol and p-cresol, and the headspace concentrations were reduced by 38.99% and 46.39%, respectively. Moreover, addition of 200mg/L kafirin could increase the odor thresholds of 3-methylindol and p-cresol to 1.50μg/L and 0.31μg/L, which were 4.59 and 1.74 times as those of the original ones separately. In order to explain the mechanism of the reducing effect of kafirin on the pit mud-like odor, the ultraviolet-visible spectrophotometers analyses at 25℃, 45℃ and 65℃ were conducted. The results showed that kafirin-3-methylindol or kafirin-p-cresol complexes could be spontaneously formed. The formation process of the kafirin-3-methylindol complex was enthalpy driven, while that of the kafirin-p-cresol was Gibbs free energy driven. In addition, molecular docking analysis showed that the hydrophobic cavity wrapped or linked 3-methylindol and p-cresol inside by spatial matching and intermolecular force, and the major forces between kafirin and 3-methylindol/p-cresol were hydrogen bonds and hydrophobic interactions. The results of this study could provide a solution for weakening the pit mud-like odor in strong flavor Baijiu, and could offer a novel method to reduce the off-odors in the food matrix.