In this study, the pine nut peptides, Lys-Asp-His-Cyc-His (KDHCH), was used as the molecule dynamics (MD) simulations subject, which has been proved that the antioxidant activity was improved after pulse electric field (PEF) treatment and the secondary structure was changed as the circular dichroism (CD) results showed. In the present study, we applied the MD simulation to discover the mechanism of the antioxidant activity improvement. The MD results showed that with the PEF treatment of 15 kV/cm, the oxygen atoms of KDHCH changed a lot, especially the atoms No.32 and No.63, of which the distance difference value was -3.02 nm, compared with the 0 kV/cm PEF treatment. The result showed an approach trend between residues Lys and His and the α-C atom of Lys, Cys and His all got closer after the PEF treatment, which means the structure became tight after the PEF treatment. However, the results of 45 kV/cm PEF treatment presented more effects on the change of KDHCH. The calculations of oxygen atoms show an approach trend between residues Lys, Asp and His. The α-C atom of Lys, Cys and His all got closer after the PEF treatment, which means the structure became tight after the PEF treatment and proved the results of the calculations of the oxygen atoms. The structures of PEF treated and untreated peptide samples were measured by 1D and 2D nuclear magnetic resonance (NMR) in order to verify the results of the molecular dynamics simulations. The 8.37-8.40 ppm (-NH- in chain) and 8.84-8.88ppm (-NH- in chain) appeared left shift, while at the 8.45-8.47ppm (-NH- in chain) occurred a right shift. The 7.82 ppm (-NH- in imidazole ring) on His shifted left after PEF treatment, which reached 7.84 ppm by the 1D-1H-NMR spectroscopy. Moreover, the long-range connectivity between -NHα (8.78ppm) on 2H-ASP and -CHα (2.72ppm) on 1H-LYS; -SH (2.50ppm) on 4H-CYS and -OH (3.53ppm) on 5H-HIS all appeared in spectra of the PEF treatment sample. This study will also be helpful to further mechanism exploration.