Objective： To study the abundance and diversity of microorganisms in different periods before， during and after fermentation of mulberry ferment by metagenome technology. Methods： To take mulberry ferment fermentation early stage （18 d）， medium-term （42 d）， late （60 d） samples and a series of metagenome sequencing steps， such as genomic DNA extraction， PCR amplification and product purification， fluorescence quantification， Illumina PE library preparation and Illumina high-throughput sequencing. After optimizing the sequencing data， the changes of bacteria and fungi composition and diversity in the fermentation process of mulberry jiaosu were studied. Results： The bacterical diversity of mulberry jiaosu was larger than that of fungal diversity by metagenome technique， and the analysis of microbial diversity in the genus level showed that the Lactobacillus was the dominant bacterium in the fermentation process of mulberry jiaosu. The yeast was the predominant bacterium（92.16%） in the prophase of fermentation. Conclusion： The dynamic changes and diversity mechanism of mulberry jiaosu 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 mulberry jiaosu.