Goat and cow milk are two major sources of infant formula, but they differ significantly in their nutrient composition. Therefore, to enable more precise infant nutrition, improve health outcomes, and provide a reference for infant formula design and allergy research, the digestion characteristics, peptide release patterns, and allergenic differences between stage 1 goat (GMF) and cow (CMF) milk-based infant formulas were investigated. An in vitro infant gastrointestinal digestion model was used, combined with degree of hydrolysis (DH) analysis, protein electrophoresis, confocal laser scanning microscopy, and peptidomics techniques. The results revealed that there were no significant differences in DH between GMF and CMF during the gastric and intestinal digestion stages (P>0.1), but the particle size of the digesta was smaller in the GMF than that in CMF during gastric and small intestinal digestion. A total of 343 and 465 peptides (<25 AA) were identified among the intestinal digesta of GMF and CMF, respectively. Among them, the proportion of short peptides (3~4 AA) was significantly higher in GMF (82.30%) than that in CMF (75.60%) (P<0.1). Furthermore, the number of potentially allergenic peptides was higher in GMF than that in CMF, but the relative abundance of the most abundant potentially allergenic peptides showed the reverse pattern (P<0.1). These results indicate that GMF might provide superior digestive efficiency compared to CMF, while the different types and quantity of allergenic peptides produced during simulated infant gastrointestinal digestion might account for the distinct allergenic risks between GMF and CMF. These findings offer a theoretical foundation for the formula design and precise allergen regulation of infant formulas.