In this study, a peptide-based method employing ultra high performance liquid chromatography electrostatic field orbitrap high-resolution mass spectrometry and triple quadrupole mass spectrometry was developed for quantification of A1type and A2-type β-casein in milk from Yak, cows, and their offspring of crosses, Pien-niu. The specific peptides of A1-type and A2-type β-casein were screened and confirmed by protein software after analysis of high-resolution mass spectrometry. The multiple reaction monitoring method was established based on the qualitative results, and isotope-label peptides were used as internal standards.The linear correlation coefficients of this method were >0.99. The relative standard deviations of repeatability test were 0.2-3.6%. The recovery rate ranged from 93.3 to 114.4% with relative standard deviations <6% at three different spiking levels. The method was applied to analyze 45 milk samples from different species.The results showed that β-casein in Yak and Pien-niu milk was about 30% higher than that in cow milk. Furthermore, the β-casein in the Yak milk only contains A2-type β-casein. A1-type and A2-type β-casein coexist in most samples of Pienniu and cow milk, a few samples contain only one type of β-casein. These results provide further understanding in nutritional value of milk from Yak and Pienniu.