Enzymatic browning was mainly associated with polyphenol oxidases which were able to act with phenolic compounds in the presence of molecular oxygen and decreased the commercial quality, organoleptic acceptance and nutritional value of the product. Membrane-bound polyphenol oxidase (mPPO) in Fuji apple (Malus domestica Borkh. cv. Red Fuji) was purified by using temperature-induced phase partitioning technique, ammonium sulfate fractional precipitation and DEAE Sepharose Fast Flow ion exchange column chromatography, and analyzed by using tandem mass spectrometry (LC—MS/MS). The best conditions for isolation and purification were ultrasonic extraction for 10min, 50%~80% saturation of ammonium sulfate precipitation, and gradient elution with 0.1mol/L NaCl. The mPPO was purified by 64.30 folds with a high specific activity (387032.97U/mg). The Native—PAGE and SDS—PAGE were single bands for mPPO and the purified mPPO was a dimmer of a subunit with a molecular weight of 67kDa. The results by mass spectrometry analysis and comparison in protein database showed that the purified protein was a polyphenol oxidase.