The integrated agri-aquaculture system (IAAS) has become one of the main directions for the sustainable development of agriculture because of its good ecological environmental effect and the ability to produce enough green rice to meet the market demand for high quality food. It is important to understand the structural characteristics of soil bacterial community in this compound system for the improvement of planting and breeding and the realization of ecological regulation. In this study, Illumina high-throughput sequencing was used to compare the surface soil and rhizosphere soil bacterial community structure among rice-turtle co-culture (R-T) and rice monoculture (R-M), and provide the theoretical basis for the accumulation of data of rice-turtle co-culture ecology and the optimization of production technology for comprehensive cultivation of rice turtle co-culture. The results showed that Proteobacteria, Acidobacteria, Bacteroidetes, Nitrospirae and Chloroflexi were the main phyla in all paddy soil. Compared with R-M, the relative abundance of Chloroflexi, Nitrospirae and Acidobacteria increased and the relative abundance of Proteobacteria and Bacteroidetes was reduced in the surface soil of the R-T. In rhizosphere soil, compared with R-M, the relative abundance of Nitrospirae, Bacteroidetes and Proteobacter increased, and the relative abundance of Chloroflexi and Acidobacteria reduced in R-T treatments. The main genera were Acidobacteria bacterium_uncultured, Nitrosomonadaceae_uncultured, Nitrospiraceae_uncultured, Geobacter, Gemmatimonadaceae_uncultured and Xanthomonadales_norank. In the two models, the relative abundance of Nitrospiraceae_uncultured and Geobacter in rhizosphere soil was significantly different (P<0.05), and the relative abundance of Nitrosomonadaceae_uncultured, Nitrospiraceae_uncultured, Gemmatimonadaceae_uncultured and Acidobacteria bacterium_uncultured in the surface soils was significantly different (P<0.05). PCA and cluster analysis showed that R-T treatments exerted a significant effect on the bacterial community structure of surface soils, and also affected the rhizosphere soil bacterial community structure to a certain extent. Overall, this study provides microbial ecological evidences for the advantages of rice - turtle integrated system over rice monoculture.