Liuyang fermented soybean is a representative of our country homology of medicine and food with thousands years of history. Being more opening of the process，microbial diversity have a significant impact on material transformation and formation of flavor before drying processing. In this paper, 454 high-throughput pyrosequencing was studied in traditional process cycle of bacterial, fungal diversity. The results show that Fermenting microorganism type difference before and after 3d is not great, but continue to fermentation after 15d, either bacteria or fungi  compared LY01, LY02 to show more diversity,mainly dominated Rhizopus，Aspergillus，yeast ; As to bacterium diversity, its number is more numbers at 15d fermentation compared with LY01、LY02。Bacillus and Lactic acid bacterium have appeared in post-fermentation stage . This difference in microbial diversity fermentation caused by the accumulation affect the product quality and efficacy needs further study, its standardized  production should be paid close attention.