Background: α-lactalbumin and β-lactoglobulin in whey protein account for a high proportion of milk protein and are the main allergens in cow milk. With increasing prevalance in China, there are limited data of epitope information on Chinese infants and children with cow’s milk allergy. Methods: In this study, affinity-purified polyclonal IgE/IgG antibodies from cow milk allergic subjects were used to screen a phage display library containing 12 amino acid random peptides as fusions to a coat protein, 140 unique peptide sequences were identified. The bioinformatical tools with DNAman alignment tool and Pepitope Server were used to identify linear and conformational epitopes, respectively. In addition, peptide microarrays covering α-lactalbumin and β-lactoglobulin sequences were used to validate linear epitopes. Results: We found no significant difference in IgE and IgG epitope recognition profiles between infant and children patients. Some important regions were identified in both IgE and IgG epitopes, and some linear epitopes are components of conformational epitopes. Conclusion: The coupling of phage display with high-throughput sequencing is a potential method to identify the epitope.