Abstract: Rice-turtle integrated system refers to a green, efficient and ecological breeding technology in modern agriculture. In the multiple species coexistence system, the turtles take the field pests and weeds as the food, while the rice absorbs the residues and excrement as the organic fertilizers in the paddy fields. Among them, the soil microorganisms can greatly contribute to the biodiversity of ecosystem functions and nutrient cycling in agroecosystems. However, only a few studies were focused on the effects of rice-turtle mixed cropping on the soil microbial community structure and functional characteristics, together with the driving factors. In this study, a systematic analysis was implemented to determine the response characteristics of soil bacterial-fungal community structure and diversity to the rice cultivation system using Illumina high-throughput sequencing. The correlation analysis was also obtained between soil physical/chemical properties and microbial community structure. The results showed that: 1) The Rice-Turtle Integrated system (RT) was beneficial to promote the soil nutrient contents and fertility. Specifically, the contents of Soil Organic Matter (SOM), Total Potassium (TK), Alkali-hydrolyzed Nitrogen (AN), Available Phosphorus (AP), and Available Potassium (AK) in the soil significantly increased by 17.82%, 15.15%, 13.80%, 37.37%, and 21.57% under the RT (P<0.05), compared with the Rice Monoculture system (RM). 2) The soil microbial richness and diversity were improved to change the microbial community structure in the RT. In the soil bacterial community, the Abundance-based coverage estimators (ACE), Chao1, Simpson, and Shannon indexes increased by 2.53%, 1.98%, 1.01%, and 1.76%, respectively. In the fungal community, the ACE, Chao1, and Shannon indexes increased by 7.70%, 7.90%, and 4.89%, respectively. At the same time, the relative abundance of Proteobacteria, Acidobacteriota, Chloroflexi, Ascomycota, and Rozellomycota increased by 6.42%, 1.16%, 1.79%, 0.44%, and 2.96%, respectively. By contrast, the abundance of Desulfobacterota, Crenarchaeota, Basidiomycota, Chytridiomycota, and Mortierellomycota decreased by 3.68%, 6.46%, 0.22%, 2.52%, and 1.26%, respectively. 3) Microbial molecular ecological networks were used to intuitively demonstrate the complex ecological interactions among microorganisms and their responses to environmental changes. The topological structure, modularity, and network composition were then selected to better reflect the relationship between the microbial community and the niche functions. The network analysis showed that the co-cropping system was strengthened the relationship between communities, leading to the high complexity of microbial network with the total number of nodes and edges, the average clustering number, as well as the modularity of bacterial microbial network. Nevertheless, the number of nodes decreased in the fungal microbial network, whereas there was an increase in the number of edges and positive interacting microorganisms, indicating the enhanced collaboration among microorganisms. 4) The redundancy analysis showed that the different soil physical and chemical properties posed the different effects on the dominant genera of microbial communities. The contents of SOM, TK, and AK were the main environmental factors on the bacterial community structure, whereas, the TK, AK, and AP contents were dominated the fungi community. In conclusion, the rice-turtle integrated system can be expected to enhance the soil fertility, the soil microbial community, the microbial richness, and the closer relationship between microbial communities. This finding can also provide an important scientific basis to explore the reasonable cultivation mode in paddy fields.