In order to study the free radical scavenging capacity and molecular structures of baicalein and scutellarein,the structure-activity relationship of these two molecules was analyzed.The geometric structures of the compounds were optimized by DMol3 code based on density functional theory.The theoretical parameters of the atomic charge distribution,the distribution of molecular frontier orbital,the energy difference and Fukui functions were calculated.Meantime,superoxide anion free radical and 1,1-diphenyl-2-pierylhydrazyl radical (DPPH) methods were used to determine the scavenging capacity of the compounds.The results showed that the scavenging rate of DPPH radicals and superoxide anion radicals increased with the increase of sample concentration,and had a dose-effect relationship.The radical-scavenging activities in the order of baicalein ＞scutellarein ＞ BHT were showed.The p-π conjugation of the hydroxyl oxygen atom influenced the certain ability to repelling electrons in the molecular structures of baicalein and scutellarein based on the data of the atomic charge distribution,the distribution of molecular frontier orbital,the energy difference and Fukui functions.Hydroxyl groups were more susceptible to attack and exhibit free radical scavenging activity.The oxygen atom in the phenolic hydroxyl group of the molecule structure of the samples may be the reaction active sites where the electrophilic reaction occurred.These results offer useful theoretical bases for the research and application of antioxidant activities of substances containing such molecular structures.