In order to fully explore the bacterial diversity in fermented food with Inner Mongolian characteristics， the bacterial community structure of different fermented food was compared. The composition and structure of bacterial communities in fermented dairy products （Cheese1， Cheese2 and Mike_cake） and fermented meat product （fermented sausage， Mutton_jerky and Beef_jerky） were analyzed based on high throughput sequencing. A total of 194 568 effective sequences and 237 OTUs were obtained. The results showed that the Shannon diversity index for fermented meat products was higher than that for fermented dairy products. The microbiota of different fermented products were significantly different. Two bacterial phyla， Firmicutes was the predominant phylum in fermented dairy products. while Firmicutes and Proteobacteria dominated the microbiota of fermented meat products； At the genus level， Lactobacillus was dominant in fermented dairy products， Pseudomonas was the major bacterial population in fermented meat product， Lactobacillus was a subdominant genus. At the species level， the dominant strains of dairy and meat products could not be determined because of the high content of undetected bacteria， but Lactobacillus sakei had a higher content in fermented dairy and meat products. The 16s predictive function analysis showed that most of the bacteria in traditional fermented food were related to the transport and metabolism function， such as Lipid transport and metabolism and Amino acid transport and metabolism.