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As a valuable natural antioxidant, sesaminol can be used in food and medicine industries, but it is trace in sesame seeds and oil, and it is feasible to prepare sesaminol from sesaminol triglucoside (STG) which is abundant in defatted sesame cake. Therefore, in order to establish an effective enzymatic preparation method and elucidate the antioxidant structure-activity relationship of sesaminol, a suitable glycosidase for preparing sesaminol from STG were screened, enzymatic hydrolysis was optimized by single-factor test and response surface methodology, and finally, the structure-activity relationship of sesaminol was illustrated by comparative molecular field analysis (CoMFA). These results suggested that β-galactosidase was the optimal glycosidase for enzymatic hydrolysis of STG to prepare sesaminol. Under the optimal conditions of a reaction temperature of 50°C, reaction time of 4.0 h, pH of 5.5, substrate concentration of 1.0 mg/mL, and enzyme dosage of 20 mg/mL, the conversion rate of sesaminol was 98.88±0.67%. Sesaminol displayed excellent antioxidant ability in 2,2-diphenyl-1-picrylhydrazyl (DPPH, IC50 = 0.0011 mg/mL), 2,2'-azinobis-(3-ethyl-benzothiazoline-6-sulfonate) (ABTS, IC50 = 0.0021 mg/mL) radical scavenging activities and Ferric reducing antioxidant power (FRAP, 103.2998 mol/g) compared to other sesaminol derivatives. According to －log (IC50 of DPPH) and －log (IC50 of ABTS), CoMFA models were successfully established based on Q2 >0.5 (QDPPH2 = 0.558, QABTS2 = 0.534). The active site of sesaminol tended to be located on the hydroxyl group of the benzene ring (R1 position). A positive correlation between the bulky and positively charged groups at the 1H, 3H-furo [3, 4-c] furan group, the small, negatively charged groups at the R1 position and the antioxidant activity of sesaminol. This study provides an effective method to prepare sesaminol, reveals the structure-activity relationship of sesaminol and provides theoretical basis to design the novel compound.