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To increase moisture of brown rice before germination, traditional soaking method provides a suitable environment for the growth of microorganisms, and segmented moisture conditioning method has no proper disinfection technique, which brings potential safety hazard to germinated brown rice. Therefore, an ozonated water treatment technique was proposed to enhance safety of brown rice before and after germination. The segmented moisture conditioned brown rice was selected as raw materials, with Design-Expert 8.0.6 software, a central composite rotatable orthogonal experimental design with four factors and five levels was employed to study effect of brown rice moisture content, initial mass concentration, treatment time and temperature of ozonated water on disinfection rate in aerobic plate count and germination rate of brown rice, and mathematical models for effect of each parameters on disinfection rate in aerobic plate count and germination rate were established. The mathematical models were extremely significant and parameters were optimized to increase disinfection rate in aerobic plate count above 97% and germination rate above 90%, and brown rice moisture content of 27.5%, initial mass concentration, treatment time and temperature of 4.7mg/L, 6.5min and 29.5℃ were decided to be optimal levels. Under this treatment condition, actual disinfection rate in aerobic plate count and germination rate were (97.49±0.11)% and (91.89±0.26)%. Compared with segmented moisture conditioning method without disinfection treatment, germinated brown rice produced with ozonated water treatment technique had significantly reduced amount of aerobic plate counts (P<0.01), and germination rate and γ-aminobutyric acid content were increased by 0.49% and 1.23mg/(100g). These verified that ozonated water pretreatment effectively disinfected aerobic plate count and increased germination rate of brown rice, which offered a basis for safety production of germinated brown rice.