Abstract: In present study, quinoa and black oat were complexed to fermented with Lactobacillus kisonensis (JCM15041) based on the contents of polyphenols and flavonoids as response values. To optimize the fermentation process, the single factor experiment was used to obtain the optimized range of fermentation parameters such as raw material ratio (quinoa: black oat), liquid to material ratio, inoculation amount and fermentation time, then the response surface experiment (four-factors and three-levels) was used to establish optimization fermentation condition. Our results showed that raw material ratio (quinoa: black oat), liquid-solid ratio, inoculation amount and fermentation time significantly affected the enrichment of polyphenols and flavonoids in complexed grain fermentation. The optimal fermentation conditions were as follows: raw material ratio (quinoa: black oat) 1:3.4 (g/g), liquid-solid ratio 7.5:1 (mL/g), inoculation amount 4.9%, fermentation time 36.5 h. Under these fermentation conditions, the contents of polyphenols and flavonoids were 295.3 and 256.3 mg/100 g, respectively, which were significantly higher than those of unfermented combined grain group (the contents of polyphenols and flavonoids were 216.2 and 202.4 mg/100 g, respectively) (P<0.05), and also higher than those of quinoa or black oat fermentation alone groups (polyphenols contents were 256.7 and 255.3 mg/100 g respectively, flavonoids content were 209.0 and 163.3 mg/100 g, respectively) (P<0.05). Compared with single grain fermentation, the fermentation of quinoa-black oat complexed grain with Lactobacillus kisonensis was more effective to the enrichment of polyphenols and flavonoids, and the fermentation products could be used for the development of functional grain food.