Rice-turtle integrated system is a green and high-efficiency ecological agricultural system. However, there are few studies on the effects of rice-turtle co-cropping on soil microbial community structure and functional characteristics and its driving factors. Illumina high-throughput sequencing technology was used to analyze the changes of soil bacterial and fungal community structure in paddy soils treated with rice monoculture system(RM) and rice-turtle integrated system(RT). The correlation between soil physical and chemical properties and microbial community structure was further analyzed. The results showed that: (1) Rice-turtle integrated system was beneficial to increase soil nutrient contents and improve soil fertility. The contents of SOM, TK, AN, AP and AK were significantly increased by 37.72%, 15.15%, 13.80%, 37.37% and 21.57% (P < 0.05). (2) Rice-turtle integrated system could increase soil microbial richness and diversity, and changed the microbial community structure. The relative abundance of soil Proteobacteria, Acidobacteriota, Ascomycota and Rozellomycota increased by 6.42%, 1.16%, 0.44% and 2.96%, respectively. And the relative abundance of Basidiomycota decreased by 0.22%. (3) Rice-turtle integrated system changed the interaction pattern of microbial communities, enhanced the relationship between soil bacterial and fungal communities, which was conducive to the stability of microbial community structure. (4) The contents of SOM, TK and AK were the main environmental factors affecting the change of soil bacterial community structure, while the contents of TK, AK and AP were the main factors affecting the fungal community structure. In conclusion, the application of rice-turtle integrated could reduce the input of chemical fertilizers and pesticides, improve soil fertility of paddy fields. At the same time, co-cropping was conducive to improving the structure and diversity of soil microbial communities, increasing soil beneficial flora, and maintaining the stability of rice field ecosystems. This study provides an important scientific basis for exploring scientific and reasonable paddy field cultivation mode.