Abstract: In this study, maillard reaction was used to modify whey protein isolate (WPI) with microwave assistance. The effects of microwave power, microwave heating time, pH, and mass ratio of lactose to whey powder on the functional properties of whey protein maillard reaction products (WPI-MRPs) were systematically investigated by using emulsification and antioxidant activity as the main indexes. The process was optimized, the secondary structure and amino acid composition during microwave treatment were also analyzed in details. The optimized microwave heating conditions are as follows: pH8.5, whey protein-lactose mass ratio 5:5, microwave heating time 7 min. The emulsification activity index, emulsifying stability index and DPPH free radical scavenging rate of the obtained MRPs was 0.35 m²/g, 88.39 min and 6.60%, respectively. The infrared spectroscopy data indicated that microwave heating could promote the maillard reaction process, during the process increases in the contents of hydroxyl and carbonyl groups were observed, and complex maillard intermediates and aldehydes and ketones were produced. Meanwhile, transformation of the protein secondary structure from a compact to a loose “swelling” structure could be also promoted. During the transformation, most of the tightly ordered structure firstly transforms into a loosely ordered structure, and then into a loosely disordered state, accompanied by a small part of the tight ordered structure changed to each other after a long time heating. In addition, amino acid analysis further confirmed that the reaction would result in a decrease in total amino acids content due to participation of free amino acids in WPI during maillard reaction.