The in vitro simulated gastrointestinal digestion characteristics and peptide profile of partially dephosphorylated β-casein (PDP-BCN), prepared enzymatically, were determined via dynamic light scattering (DLS), confocal laser scanning microscopy (CLSM), and liquid chromatography-tandem mass spectrometry (LC-MS/MS). The results demonstrated that the flocculated structures and particle size formed by PDP-BCN in simulated infant gastric fluid were significantly smaller than those of native β-casein (β-CN), making it more easily digested into smaller particles. Moreover, during simulated infant gastrointestinal digestion, PDP-BCN degradation generated 880 peptide fragments, far exceeding the 533 peptides produced by native β-CN. This difference in peptide fragments was particularly notable at the N-terminal region of the protein. Additionally, PDP-BCN degradation yielded 8 unique bioactive peptides and 137 peptides with potential bioactivity, exceeding both the number and functional diversity of peptides derived from native β-CN. Therefore, PDP-BCN exhibited significant advantages over native β-CN in terms of digestibility. This study provides a theoretical basis for the future application of PDP-BCN as a novel protein ingredient in infant formula.