Objective: To explored the microbial diversity and community structure of traditional fermented raw cheese of yak milk in Tashkorghan Pamirs Xinjiang. Methods: 6 raw cheese samples were collected from different herdsmen's families. The microbial diversity was analyzed by high-throughput sequencing technology. At the same time， the traditional yak milk fermented cheese samples were selected and isolated by pure culture. The species of bacteria and yeast were identified by traditional classification， 16S rDNA sequencing and 26S rDNA D1/D2 spacer sequencing. Results: The optimized sequence 945 432 was obtained by sequencing the V3-V4 region of 16S rDNA gene. The optimized sequence 1 302 962 was obtained by sequencing the its region of fungi. At the genus level， Lactobacillus and Streptococcus belonging to Firmicutes were the dominant bacterium， Kluyveromyces， Torulaspora， Issatchenkia and unclassified dipodascacease belonging to Ascomycotea were the dominant fungi. According to PCoA analysis， the community structure of the six samples had both similarities and differences. 52 strains of bacteria were isolated on MRS and MC medium and 46 strains of yeast were isolated on YGC medium. Through the analysis of bacterial 16S rDNA sequence and fungal 26S rDNA D1/D2 compartment sequence， 52 strains of bacteria were classified into 7 genera and 11 species. They were Enterococcus durans， Enterococcus faecium， Bacillus tropicus， Bacillus cereus， Bacillus paramycoides， Pseudomonas helleri， Lactobacillus paracasei， Lactobacillus gallinarum， Enterobacter hormaechei， Streptomyces microflavus and Staphylococcus epidermidis. 46 yeast strains were classified into 8 genera and 9 species. They were Yarrowia lipolytica， Candida zeylanoides， Pichia fermentans， Pichia kudriavzevii， Guehomyces pullulans， Wickerhamomyces anomalus， Kluyveromyces marxianus， Issatchenkia orientalis and Saccharomyces cerevisiae. In this study， the microbial resources in traditional fermented dairy products in Tashkoghan Pamirs were analyzed for the first time. There is diversity of microorganisms in yak milk fermented milk products in this area. Further in-depth research and excavate are needed.