In this study, phage display technology combined with bioinformatics was used to identify the B cell epitopes of α-lactalbumin and β-lactoglobulin from bovine whey. The amino acid composition and spatial distribution of different types of epitopes was analyzed. The results showed that some linear epitopes were part of the conformational epitopes. IgE and IgG-binding epitopes shared some common sequences. At the same time, we identified a new linear IgE-binding epitope in β-lactoglobulin. The epitopes we obtained are candidate biomarkers for the diagnosis and prognosis of milk allergy, and can be used for guiding the development of hypoallergenic dairy products.