Abstract: To study the free radical scavenging mechanism of two types of rye antioxidant peptide, peptide R-Ⅰ and peptide R-Ⅱ, the amino acid sequences and free radical scavenging rates were determined, and the optimized geometric structure, the atomic charge distribution, Fukui index f⁰(r), the distribution of frontier molecular orbital (HOMO&LUMO) and the energy difference (ΔE) were calculated using the quantum chemical calculation methods. The results showed that both types of rye antioxidant peptide had the ability to scavenge free radicals, with rye antioxidant peptide R-Ⅰ having a stronger antioxidant ability (P<0.05). The IC₅₀ (half maximal inhibitory concentration) of peptide R-Ⅰ for scavenging hydroxyl radicals, DPPH radicals, and superoxide anion radicals were 0.175±0.0053, 0.306±0.012, 0.065±0.0013 mg/mL, respectively. According to the quantum chemistry calculation, the active sites of antioxidant peptide R-Ⅰ were the amide group of N-terminal glutamine, the carboxyl group of C-terminal leucine, and the guanidine group of arginine; the active sites of antioxidant peptide R-Ⅱ were amino group of leucine, guanidine group of arginine, the peptide binding site between Leu-1 and Arg-2, the peptide binding site between Arg-2 and Ile-3 and the peptide binding site between Pro-5 and Thr-6. These data revealed the free radical scavenging mechanism of rye antioxidant peptides.