The objective of this study was to explore and compare the effect of different thermal treatments on the stability of koumiss proteins. It measured indicators of koumiss quality at different heat treatment conditions， and then the suspension stability of koumiss protein as well as the denaturation degree of whey protein were observed by SDS-PAGE. Fourier transform infrared spectroscopy was employed to investigate the variation of secondary structures. The results showed that thermal treatment from 65 ℃ to 90 ℃ had no effect on the acidity and pH value of koumiss， but the centrifugal suspension content， denaturation rate and the proportion of secondary structures of koumiss protein after heat treatment changed significantly compared with those without heat treatment (P<0.05). The variation of β-sheet played an important role in the degree of thermal aggregate of koumiss protein. With the increase of the degree of thermal treatment， the viscosity of koumiss and the degree of denaturation of whey protein increased continuously， and the denaturation rates were 38.52%， 40.88%， 50.94% and 69.03% respectively， which showed an accelerated increasing trend. After heat treatment at 90 ℃ for 5 min β-Lactoglobulin disappeared and the stability of whey protein was seriously damaged. Moreover， the properties of zeta-potential， protein suspension stability and β-sheet structure showed a trend that increased firstly and then decreased. Appropriate thermal treatment could improve the stability of koumiss proteins.