Rotation is an important method to improve land utilization and the economic benefits of aquaculture. Shrimp vegetable rotation is a new farming and planting rotation model. The purpose of this study is to reveal the community of microorganisms in pond sediments under shrimp-vegetable rotation and provide theoretical basis for maintaining soil fertility. In this study, three groups were set: cultivated areas (CC, shrimp-vegetable rotation mode), uncultivated area (CG, shrimp farming and fallow mode), and flooded area (CS, continuous shrimp farming mode). Diversity and community composition of microorganism communities were displayed using real-time PCR and high-throughput sequencing platforms. The results showed that the shrimp-vegetable rotation significantly reduced the content of total nitrogen (TN, compared with CG and CS, CS has dropped by about 50% and 80%, respectively),total carbon (TC, compared with CS, CS has dropped by about 50% and 70%, respectively) and total phosphorus (TP, compared with CG and CS, CS has dropped by about 60%) in the sediment and removing excess nutrients in the aquaculture environment. The relative abundance of Proteobacteria and Gemmatimonadetes phylum was significantly higher in the CC and CG groups than in CS. And the majority of denitrifying bacteria are concentrated in the Proteobacteria that increased abundance of denitrifying bacteria confirms results of increased copy number of nosZ and phoD genes. Herein, a conclusion was drawn that shrimp-vegetable rotation had stronger restoration ability of soil bacterial diversity and soil fertility than the other two farming mode. Also, the rotation mode promoted a good ammonia nitrogen cycle. This study will provide a scientific basis and data support for the application of shrimp vegetable rotation.