Abstract: Abstract: Milk is rich in nutrition, and it is a good medium for microorganisms, therefore, heat treatment are commonly used to sterilize in the process of liquid milk processing. Although the heat treatment can kill microorganisms in milk, it is possible to change the nutritional value and functional properties of milk, so it is essential to study the effects of heat treatment on the structural and properties of milk proteins, especially on whey protein monomers and casein monomers. The heat treatment of milk is generally carried out by pasteurized, and the ultra-pasteurized milk is also very popular recently. At present, there are few reports on the effects of heat treatment on the structural properties of milk whey protein. In this paper, defatted milk obtained by centrifugation through fresh milk as raw material. Then, the skim milk is subjected to low temperature long-term and high-temperature pasteurization and ultra-pasteurization treatment, and the casein are extracted by isoelectric precipitation, and finally whey protein was detected by different detection methods and techniques. So the effects of pasteurization and ultra-pasteurization on the structure and thermal stability of whey protein were discussed. The results of the protein concentration and SDS-PAGE gel electrophoresis showed that the whey protein content extracted by the isoelectric point method after heat treatment was high and the casein content was substantially absent. The results of infrared spectroscopy showed that pasteurization had little effect on the secondary structure of whey protein, while the content of α-helix in whey protein was significantly reduced after ultra-pasteurization treatment, and the random curl content increased significantly, it indicated that there was no significant change in the secondary structure of whey protein after pasteurization treatment, and the development of disordered structure changed from ordered structure to disordered structure after superpasteurization treatment, thereby improving the thermal stability of whey protein. Fluorescence analysis showed the whey protein sample heat-treated at 121 ℃ for 5 s was red-shifted, indicating that super-pasteurization greatly changed the secondary and tertiary structure of whey protein, it is shown that too high temperature will destroy the tertiary structure of whey protein and increase the polarity of the protein microenvironment. DSC analysis showed thermal denaturation of whey protein sample treated at 121 ℃ for 5 s, the peak temperature was 99.9 ℃, which was higher than that of the pasteurized whey protein sample, indicating that the stability of the whey protein sample after the ultra-pasteurization treatment was significantly improved. This may be due to the ultra-high temperature treatment to fully denature the whey protein and increase the disordered structure in the protein, which also indicates that the whey protein aggregate formed by ultra-high temperature was heat stable and the degree of denaturation was irreversible. The production and demand of dairy products in China are very large and the consumer groups are extensive. Therefore, it is very important to carry out research on the related technology of dairy processing to ensure the quality and safety of dairy products and promote the healthy and rapid development of China's dairy industry.