Perilla seed meal was used as raw material, which was mixed fermented by lactic acid kluyveromyces and bacillus coagulans. The process of fermentation was optimized through controlling bacteria ratio，inoculation amount，ratio of solid to water, with the content of small peptides as the index.The results showed that when the ratio of lactic acid kluyveromyces to bacillus coagulans was 1∶1, inoculation amount was 12%, ratio of solid to water was 1∶2.5 g/mL, fermented at 33 ℃ for 2 d, the concentration of small peptides reached to 4.07 mg/mL, which was increased by 26.40% compared with that before fermentation.