Phlorizin (PHL) is a natural compound with strong antioxidant properties mainly found in apples. In this paper, the interaction mechanism of PHL with pepsin and trypsin was comparatively evaluated by computer simulation, fluorescence spectra, circular dichroism (CD), and fourier transform infrared (FT-IR) spectra at a molecular level. Fluorescence spectra showed that PHL quenches the pepsin/trypsin by static quenching. Thermodynamic parameters indicated that PHL binds to pepsin mainly through hydrogen bonds and van der Waals forces, and that of trypsin was electrostatic forces. The ground state complexes PHL and protease have a moderate affinity of 105 L/mol PHL binds more strongly to trypsin than to pepsin. CD and FT-IR spectra results showed that pepsin/trypsin decreased the β-sheet content and slightly changed its secondary structure upon PHL. These experimental results are mutually verified with the predicted computer-aid simulation results. Upon PHL and trypsin binding, the antioxidant capacity of PHL was elevated. Nevertheless, the antioxidant capacity of PHL was decreased after binding to pepsin. This work elucidates the binding of PHL binding mechanisms to pepsin/trypsin and provides useful information for the digestion of PHL to improve the application of PHL in food processing.