Polyphenol oxidase (PPO) easily causes fruits and vegetables to lose their color and nutritional value. As a non-thermal process, high-pressure processing (HPP) showed different inactivation effects on endogenous enzymes. In this work, soluble PPO (sPPO) and membrane-bound PPO (mPPO) from ‘Lijiang snow’ peaches were purified, and then the effect of high pressure on the conformation of sPPO and mPPO was investigated and compared at the molecular level. The maximum activation of sPPO and mPPO by 11.2% and 4.8% was observed after HPP at 200 MPa, while their activities both gradually decreased at 400 MPa and 600 MPa; in particular, the residual activities of sPPO and mPPO at 600 MPa for 50 min were 41.42% and 72.95%, respectively. The spectroscopic results indicated that the secondary structure of PPOs was little affected by HPP, but HPP led to obvious changes in their tertiary structure. The simulations showed that the decreasing distance between the copper ion and His residue in the copper-binding region of two PPOs at 200 MPa was favorable to catalytic activity, while the increasing distance between copper ions and His residues and the disordered movement of the loop region above 400 MPa were unfavorable. In addition, the structure of sPPO was relatively looser than that of mPPO, and high pressure showed a more significant effect on the conformation of sPPO than that of mPPO. This study clarified the effect of HPP on PPO’s structure and the relationship between its structure and activity and provided a basis for the prevention of enzymatic browning.