High pressure processing (HPP) exhibited different effect on polyphenol oxidase (PPO), but the conformational changes was not clear yet. In this study, molecular dynamics simulation combined with spectroscopic experiments were used to explore PPO conformational changes under high pressure at the molecular level. The simulation results showed that high pressure decreased volume and hydrogen bonds, induced changes in active center and movement of loop. Especially, the conformational changes under 200 and above 400 MPa were different. Under 200 MPa, the distance between His 61 and Cu decreased by 0.4 Å, active pocket was exposed, substrate channel became larger. However, the distance increased by 6.1 Å under 600 MPa, active pocket moved inward, substrate channel became narrower. Docking results of 200 and 600 MPa had the highest and lowest binding affinity, whose T-score was 4.657 and 4.130, respectively. These results were consistent with spectroscopic experiments of PPO after HHP.