The protective effects of the peptides Asp-Asp-Asp-Tyr (DDDY) and Asp-Tyr-Asp-Asp (DYDD) against AAPH-induced HepG2 cells are unclear. Our objective was to investigate the active sites of these peptides and their cellular antioxidant mechanism. DDDY and DYDD show a direct free radical scavenging effect in reducing ROS levels and maintained cellular antioxidant enzymes at normal levels. The quantum chemistry analysis of the electronic properties of antioxidant activity showed that DYDD has a greater energy in the highest occupied molecular orbital than DDDY, and O58-H59 and N10-H12 were identified as the active antioxidant sites in DYDD and DDDY, respectively, indicating that the inconsistent arrangement of amino acids affects the distribution of the highest occupied orbital energy as well as the active sites; thus, influences the antioxidant activity of peptides. It provide valuable insights into the antioxidant active sites of peptides.