The inactivation of polyphenol oxidase from watermelon juice with high pressure carbon dioxide (HPCD) treatment was investigated. The maximum reduction of polyphenol oxidase (PPO) activity inactivated by HPCD treatment was 95.8% at 30 MPa and 50°C for 30 min, which was far higher than 50.9% of control treatment at 50°C for 30 min. The inactivation of PPO was adequately described by a two-fraction model, which indicated that a labile and stable fraction might present in PPO from watermelon juice. The kinetic rate constants k L and k S of labile and stable fractions were 1.976 and 0.041 min −1 by HPCD treatment of 30 MPa and 50°C. And the labile fraction was easier to be inactivated by kinetic analysis. HPCD treatment with the combined effects of pressure, temperature, pH reduction, and time was stronger to inactivate PPO from watermelon juice than control treatment at the same temperature.