Abstract: In present study, the germinated brown rice was processed with hydrogen-rich water (HRW), the germination potential, sprouted rate and total flavonoid content were determined under different HRW concentration, germination temperature and soaking time. After the establishment of optimal germination processing conditions via single factor and response surface experiments, the effects of HRW on the ultrastructure of brown rice bran and partial thermal property parameters of germinated brown rice were investigated. The results showed that the optimal processing conditions for HRW germinated brown rice were as follows: Soaking time 13 h, germination temperature 29 ℃, HRW concentration 1.51 mg/L. Under this condition, the germination potential of HRW germinated brown rice was 67%, germination rate was 84% and total flavonoid content was 186.5 mg/100 g, which were significantly higher than those of pure water germinated brown rice (germination potential 46%; germination rate 70%; total flavonoid content 130.3 mg/100 g) (P<0.01). SEM results showed that the bran structure of HRW germinated brown rice was more porous than that of pure water treatment group. The thermal physicochemical analysis results showed that the enthalpy of gelatinization of HRW germinated brown rice was significantly lower than that of brown rice and pure water germinated brown rice (P<0.05). The HRW processing technology of germinated brown rice exhibited application value due to the effective improvement on the germination efficiency, functional activity and gelatinization characteristics of germinated brown rice.