As we know, milk and yogurt have good nutritional value and it is reported that some peptides can induce tolerance to alleviate or eliminate cow's milk allergy (CMA). However, there is a lack of detailed information on the peptides after digestion which could induce tolerance. In this study, the distribution pattern of digested proteins was detected during gastrointestinal digestion in infants and adults by Tricine-SDS-PAGE and RP-HPLC, and the digestive products were transported by the model of Caco-2 cells and the sequence of peptides was identified by LC-MS/MS. Residual allergenicity was evaluated by indirect ELISA during gastrointestinal digestion and the released peptides were aligned with T cell/IgE epitopes and biological functions by prediction software and previous information. These results indicated that the major allergens in yogurt were more easily digested with stronger transport capacity and had lower IgE-binding capacity. We obtained 113 peptides from the major allergens in the digested products and 38 of these peptides existed in all the digested products, among which 13 peptides had specific biological functions, such as ACE-inhibitory, antimicrobial and DPP-IV inhibitory properties. Although there was no obvious difference in the number of epitopes between fresh milk and yogurt, the difference in the properties and content of specific peptides might be the key factor for the difference in allergenicity. Most importantly, 11 peptides that contained T cell epitopes but not IgE epitopes might induce immune tolerance in CMA, which should be confirmed further.