The desensitization effect of the hypoallergenic infant formula products is critical for production quality, and establishment of sensitive and accurate determination method of allergens, such as αs1-casein and αs2-casein, remains challengeable in the field of infant formula industry. Therefore, the objective of this study was to identify specific peptides (YLGYLEQLLR and FALPQYLK) from αs1-casein and αs2-casein in infant formula by orbitrap high resolution mass spectrometry (Orbitrap MS), then establish an analytical method for the qualitative and quantitative determination of αs1-casein and αs2-casein based on extended specific peptide-isotope-labeled internal standard dilution-LC-MS/MS. Specific peptides obtained by trypsin enzymolysis of hypoallergenic infant formula were separated by Waters Acquity LC HSS T3 column, and analyzed under ESI positive ion mode using multi-reaction monitoring (MRM). The specific peptides of αs1-casein and αs2-casein exhibited linear relationships within the concentration range of 0.0025–1.5 μmol/L and correlation coefficients were above 0.99. The detection limits of αs1-casein and αs2-casein were 0.3 mg/kg, with quantification limits of 1.0 mg/kg, respectively. The average recoveries were 83.5%–87.3% (αs1-casein) and 80.1%–84.4% (αs2-casein), with RSDs of 2.3%–3.7% (αs1-casein) and 2.5%–5.0% (αs2-casein), respectively. Our results demonstrated that this method is capable of analyzing the content of αs1-casein and αs2-casein in hypoallergenic infant formula with excellent sensitivity and specificity.