Abstract: In order to explore the structure-activity relationship and elucidate its mechanism of action from the theoretical aspect,twelve free radical scavenging peptides were selected as the research object. Quantitative chemical calculations were carried out by using semi-empirical AM1 and density functional theory(DFT). It’s activity was measured by in vitro free radical scavenging assay,the theoretical data and experimental data were analyzed and compared. The results showed that the indole structure of Trp,the phenolic hydroxyl structure of Tyr,the hydroxyl structure of Ser and Thr,the heterocyclic structure of His,the nitrogen atom of amino group,the oxygen atom of carboxyl group and the peptide bond were all the most important active sites,playing a significant role in clearing RSP radical scavenging. The order of activity of free radical scavenging by RSP was the same as that of RSP scavenging DPPH·approximately,suggesting that the energy gap could used to determine the ability of peptides to scavenging DPPH·.