The presence of antioxidant peptides in cooked foxtail millet prolamin (CFMP) is pivotal for its ability to mitigate oxidative stress and subsequently exert an anti-diabetic effect. However, the alterations in structural characteristics and antioxidant activities of foxtail millet prolamin following cooking remain unclear. Furthermore, the identification of antioxidant peptides in CFMP targeting myeloperoxidase (MPO), a key enzyme implicated in oxidative stress, has yet to be achieved. This study aims to examine the changes in physicochemical, digestibility, and antioxidant properties of foxtail millet prolamin post-cooking, and to identify potential antioxidant peptides from CFMP targeting MPO. The findings revealed significant reductions in water and oil holding capacities, foaming and emulsifying capacities, surface hydrophobicity, and zeta potential of foxtail millet prolamin after cooking, along with a notable increase in average particle size, indicative of protein molecule aggregation and increased resistance to digestion. Three potential antioxidant peptides (IFVFPSGAG, MMFPM, and VLIPMP) were identified in CFMP hydrolysate. Molecular dynamic simulation demonstrated favorable binding interactions between all three peptides and MPO, primarily mediated by hydrogen bonds. In vitro antioxidant activity assays confirmed IFVFPSGAG as the most potent antioxidant peptide. This study sheds light on the properties of CFMP and the antioxidant potential of its derived peptides.