Abstract: The aim is to investigate the different effects of the normal heating and microwave heating on the oxidation of whey protein. In this study, the whey protein (WPI) was normally heated for 15, 30, 60 and 90min, or heated by microwave for 60, 120, 240 and 360s. The heated samples were measured to compare the changes in fluorescence spectrum, carbonyl content, sulfydryl content, bityrosine level, surface hydrophobicity and SDSPAGE. The results showed that comparing with the normal heating, the long-term microwave heating obviously improved the carbonyl content and bityrosine level of WPI and decreases sulfydryl content. The results from surface hydrophobicity and fluorescence spectrum indicated that microwave heating had an obvious influence on the space structure of WPI. The SDS-PAGE suggestd that the microwave heating had obvious production of crosslinking of WPI.