Rice-fishery integrated farming systems not only effectively reduces the use of chemical fertilizers and pesticides, but also enhances food safety and cultivation benefits, contributing to poverty alleviation, increased employment, and the resolution of abandoned farmland issues. The "rice-crayfish" and "rice-duck-crayfish" are the most typical and fastest-growing systems of rice-fishery integrated farming systems in China. Rice fields and straw provide favorable living environments and ample food for crayfish, whose necromass, excrement, and leftover feed in nutrient accumulation and cycling. Studies showed that the bioturbation and predation behaviors of crayfish could affect paddy soil microbial diversity and organic carbon accumulation, which has the importance of sustainable development in rice-fishery integrated farming systems. A field comparison experiment of rice monoculture system (RMs) and rice-crayfish farming system (RCs) to investigate the diversity of microbial communities and organic carbon sequestration in the topsoil (0-20 cm) and subsoil (20-40 cm). The results demonstrated that the RCs leaded to a 7.3% increase in topsoil organic carbon content compared to RMs, while a significant increase of 35.8% in subsoil. The fungal community diversity in the subsoil significantly decreased, with Chao, Richness, and ACE indices declining by 6.9%, 7.2%, and 8.7%, respectively, while there was no significant impact on microbial community diversity in the topsoil. The RCs notably enhanced the network size, connectivity, and average degree of co-occurrence networks for bacteria and fungi in both topsoil and subsoil, thereby improving network stability. Overall, the RCs significantly increases subsoil organic carbon accumulation and microbial community stability, promoting paddy soil biological fertility.