In order to study the changes of sea buckthorn Jiaosu fungi and their community structure during natural fermentation， the fungal rRNA gene ITS1 region was analyzed by high-throughput sequencing technology. The results indicated that 4 phyla， 16 classes， 35 orders， 71 families， 98 genera and 112 species were identified according to 97% similarity of operational taxonomic units(OTUs). The fungal community structure diversity and richness in the early fermentation stage (F22_Q) were the highest than those of the others. With the progress of fermentation， the species richness and diversity of fungal community showed a decreasing trend. At the level of fungal phylum， Ascomycota was the dominant phyla in the F22_Q and middle stage(F22_Z)， and the relative abundance ranged from 76.97% to 96.30%， Mucoromycota was absolute dominant phyla in the later stage (F22_H) and the relative abundance ranged from 2.39% to 77.50%. At the level of fungal genus， Colletotrichum was absolute dominant genus in the F22_Q and the relative abundance was 30.64%， unclassified_o_Saccharomycetales was absolute dominant genus in the F22_Z and the relative abundance was 58.06%， Mucor was absolute dominant genus in the F22_H and the relative abundance was 77.50%. The three fermentation stages could be divided into two groups， the F22_Q was clustered into one group， the F22_Z and the F22_H were clustered into one group. The samples showed significant differences(P<0.05) among Mucor， unclassified_o_Saccharomycetales and Rhodotorula. At the level of fungal species， in the F22_Q， unclassified_g_Colletotrichum was absolute dominant species and the ratio was 31%. In the F22_Z， unclassified_o_Saccharomycetales and unclassified_g_Talaromyces were the highest and the proportions were 58% and 22% respectively. In the F22_H， the proportion of Mucor_circinelloides was the highest (up to 75%)， which was the dominant position. The study provided strong support for the development of the dominant fungus community and the excavation of probiotics in the fermentation of sea buckthorn Jiaosu.