The geometry of myricetin and dihydromyricetin was optimized by DMol3 program based on DFT. The optimized structures have been proved to be stable by real frequencies obtained. The parameters of geometry optimization, vibration frequencies, atomic charges, thermodynamics, Fukui functions, and frontier molecular orbital had been obtained. The thermodynamic properties of 2 molecules were fitted and the relationship between the thermodynamic function and temperature was obtained. The correlation coefficient of the obtained equations is larger than 0.99, indicating that the function is approximately linear in the whole temperature range. The calculated results showed the O–H molecular structures were the main group affecting the antioxidant activity and the oxygen in the benzene ring is the electrophilic reaction site. Ortho-OH on the benzene formed intramolecular hydrogen bonds, which contributed to the stability of the benzene ring. It may be the active site for the occurrence of the reaction.