Purpose： In order to investigate the composition of microorganisms in apple natural fermentation Jiaosu and explore the dominant flora in different stages of fermentation. Method： The metagenomic analysis was used to analysis the composition and changes of fungi and bacteria in the three periods of pre-fermentation （10 d）， medium （20 d） and post- （35 d） of apple natural fermentation Jiaosu. The results showed that diversity analysis showed that the diversity of bacteria was higher than that of fungi. The diversity of bacteria was the highest in the early period and decreased first and then increased， slight increase in fungal diversity. In the genus level analysis， bacteria were mainly Lactobacillus， Gluconobater， Lactococcus， Weissella， Leuconosloc and Acetobacter. Among them， Lactobacillus （58.73%， 49.08%， 56.34%） and Gluconobacter（20.42%， 34.72%， 24.64%） were the dominant genus in bacteria， fungi were mainly Saccharomyces， Hanseniaspora and Zygosaccharomyce. Among them， Zygosaccharomyce （89.5%，18.2%，80.3%） and Hanseniaspor （9.7%，60.6%，8.7%） were dominant genus. Conclusion： The dynamic changes and diversity mechanism of apple ferment in the process of natural fermentation were clarified， which provided practical guidance and theoretical basis for the subsequent development of a new type of artificial controllable apple Jiaosu.