The primary aim of this study is to investigate the impact of intensive pulsed light (IPL) on the activity, structure, and physico-chemical properties of polyphenol oxidase. The results showed that the lower the concentration of PPO, the lower the intensity and fluence required inactivating 90% of PPO. With the increase of the IPL fluence, the content of ɑ-helix and β-turn decreased by 57.6% and 22.5%, and the content of β-fold and random curl increased by 58.2% and 69.0%, respectively. The endogenous fluorescence intensity decreases, which proves that IPL effectively inactivates PPO by destroying the secondary and tertiary structure of PPO. Surface hydrophobicity, free sulfhydryl content, aggregation index, and turbidity increased by 191.0%, 24.3%, 23.5%, 151.7%, respectively. The atomic force microscopy (AFM) results showed that the height distribution increased from 3 to 8 nm to 12–16 nm as the fluence increased, and the surface roughness decreased. This research provides a theoretical basis for applying IPL technology in inhibiting endogenous enzyme activity in food and controlling the browning of fruits and vegetables.