Hypoallergenic processing is an area worthy of continued exploration. In the treatment of the peanut protein (PP), pH shift was applied by acidic (pH 1.0–4.0) and alkaline (pH 9.0–12.0) treatment, after which the pH was adjusted to 7.0. Following pH-shift treatment, PP showed a larger particle size than in neutral solutions. SDS-PAGE, CD analysis, intrinsic fluorescence, UV spectra, and surface hydrophobicity indicated the protein conformation was unfolded with the exposure of more buried hydrophobic residues. Additionally, the IgE-binding capacity of PP decreased after pH-shift treatment on both sides. Label-free LC–MS/MS results demonstrated that the pH-shift treatment induced the structural changes on allergens, which altered the abundance of peptides after tryptic digestion. Less linear IgE-binding epitopes were detected in PP with pH-shift treatment. Our results suggested the pH-shift treatment is a promising alternative approach in the peanut hypoallergenic processing. This study also provides a theoretical basis for the development of hypoallergenic food processing.