Abstract: Camel milk, a characteristic dairy resource in Northwest China, is rich in bioactive peptides. Released during in vivo digestion, bioactive peptides have potential health benefits; however, systematic studies in this field remain limited. In this study, simulated gastrointestinal digestion combined with liquid chromatography-tandem mass spectrometry was used to identify and analyze peptides in camel and cow milk. Potential bioactive peptides were screened using peptide databases. The analysis identified 1074 peptides, including 561 unique to camel milk, 385 unique to cow milk, and 128 identical in both. These peptides predominantly had molecular weights of 750~1000 Da and lengths of 7~11 amino acids, most of which originated from casein. Bioactivity database analysis identified six bioactive peptides in camel milk, including two camel-specific dipeptidyl peptidase IV inhibitory peptides. The remaining four peptides, as in cow milk, had angiotensin-converting enzyme inhibitory, antimicrobial, antithrombin, and antithrombotic activities. In addition, the machine-learning-based peptide activity prediction tool, Peptide Ranker, predicted 70 potential bioactive peptides unique to camel milk and 44 unique to cow milk. These findings reveal the unique advantages of camel milk in terms of the diversity of bioactive peptide types and functional specificity. The study systematically elucidated the compositional differences of protein peptides between camel milk and cow milk, providing a theoretical basis and practical guidance for the development of novel dairy-based foods with precise nutritional functions, and contributing to the advancement of the relevant industries.