Objective To establish a qualitative and quantitative method for bovine whey protein in goat milk-based infant formula using liquid chromatography-tandem mass spectrometry (LC-MS/MS). Methods After sample treatment with dithiothreitol reduction, iodinated acetylamide alkylation, and recombinant trypsin digestion, characteristic peptides were screened using quadrupole/electrostatic field orbital trap high-resolution mass spectrometry combined with a protein database. Representative goat milk-based infant formula was adulterated with desalted bovine whey powder at common ratios, and LC-MS/MS detection was performed. Experimental conditions were optimized based on the response of characteristic peptides, and a qualitative and quantitative method for bovine whey protein was established by converting the sum of bovine α-lactalbumin and β-lactoglobulin content to bovine whey protein. Results The method demonstrated strong specificity, with detection limits of 20 mg/100g for bovine α-lactalbumin and 40 mg/100g for bovine β-lactoglobulin. The recovery ranged from 91.8% to 100.8%, with relative standard deviations ≤10.00% for both. Based on the conversion factor, the detection limit for bovine whey protein was 51 mg/100g, and the quantitative limit was 102 mg/100g. Conclusion The method is reliable and highly sensitive, enabling accurate qualitative and quantitative detection of bovine whey protein in goat milk-based infant formula.