Abstract: Aquaponics, a new type of sustainable, cyclic and zero-emission composite farming system, has become an effective method to solve the agricultural ecological crisis because of its good ecological environment effect and food safety guarantee. The 16S rRNA gene (V3-V5 region) of microorganisms in aquaculture environment and roots was sequenced by using Illumina high-throughput sequencing platform under the typical aquaculture pond mode in Northwest China. The comparison of microbial community structure and diversity showed that the total effective sequence of bacteria was 56444, and the average number of annotated OTU was 945. The dominant bacteria were phyla Proteobacteria, Bacteroidete, Firmicutes and Cyanobacteria. The dominant bacteria in MD.R and JH.R were phyla Bacteroidetes and Proteobacteria, respectively. There were 165 OTUs in the six samples with the highest OTU in JH.KX (137), the lowest one in JH.R (30), and the same OTU (85) in MD.R and JH.C. Rhizobia, fish pathogenic bacteria, cold-resistant bacteria and bacteria that decompose organism and reduce heavy metals and toxins were detected by annotating the OTUs. This study revealed the microbial community structure and its ecological regulation mechanism under the aquaponics model.