A comparative analysis of microorganism （fungi and bacteria） was carried out on two different types of Jiajiang fermented bean curd， Spicy fermented bean curd and Chinese cabbage fermented bean curd by High-Throughput Sequencing and traditional culture method. The results showed that the number and diversity of bacteria （107 CFU/g， a total of 65 OTUs） were higher than that of fungi （10-104 CFU/g， a total of 27 OTUs）. The composition of bacteria has certain similarity， and the members of Bacillus （spicy fermented bean curd 63.41%；Chinese cabbage fermented bean curd 40.06%） and lactic acid bacteria （LAB） （Spicy fermented bean curd 25.53%；Chinese cabbage fermented bean curd 33.63%） were the most abundant. But the composition of LAB in the two fermented bean curd samples was significantly different that the content of Streptococcus （11.81%） was higher in Spicy fermented bean curd but Enterococcus （20.07%） was higher in Chinese cabbage fermented bean curd. A large difference was found in the composition of fungi between Spicy fermented bean curd and Chinese cabbage fermented bean curd. Aspergillus was predominant in Spicy fermented bean curd， whereas yeast was dominant in Chinese cabbage fermented bean curd. In conclusion， this study indicated that the microorganism in Jiajiang fermented bean curd has a high diversity and complexity.