In order to clarify the impact of vegetable-fungus rotation mode on soil microorganisms，the structure and diversity of soil microbial community under four rotation modes were studied based on high-throughput sequencing technology.The results showed that the total number of fungi and bacteria OUT in soil samples under different rotation modes were 2298 and 15840 respectively；Compared with conventional rotation mode A，the total number of OUT，ACE index，Chao1 index and Shannon index of fungi of the vegetable-fungus rotation modes B，C，D decreased significantly，and the Simpson index increased significantly，but there was no significant difference in those parameters of bacteria.The contents of total nitrogen，alkali hydrolyzable nitrogen，available potassium and organic matter in vegetable-fungus rotation modes B，C，D soil were significantly higher than those in rotation mode A.The dominant community of fungi was Ascomycota，with the abundance of more than 66%. The abundance of two pathogenic bacteria(Cladosporium and Fusarium)were decreased significantly in vegetable-fungus rotation modes B，C and D.The dominant communities of bacteria were Proteobacteria，Actinbacteria，Chloroflexi and Acidobacteria，and the abundance of Sphingomonas and Burkholderia were increased significantly in vegetable-fungus rotation modes B，C，D.Cluster analysis showed that the similarity of microbial community structure was the highest under vegetable-fungus rotation modes C and D，and conventional rotation mode A could be divided into individual group which were different from vegetable-fungus rotation modes B，C，D.In conclusion，vegetable-fungus rotation can reduce the abundance of fungal community，changed the structural composition of soil microbial community，improved the abundance of beneficial bacteria and reduce the abundance of harmful bacteria.