Abstract: Integrated rice-crayfish farming system is a symbiotic ecological model applicable in paddy field cultivation that is based on the combination of rice planting and clawed crayfish breeding in waterlogged conditions. In spite of so many efforts, the effects of integrated rice-crayfish farming system on denitrifying micro-organism diversity and community structure have remained unclear. In this study, we analyzed soil samples from both consecutive treatment of integrated rice-crayfish farming system (CR) in 2014-2016 and traditional paddy field (MR) treatment in order to investigate the effects of integrated rice-crayfish farming system on microbial diversity and community structure of nirK denitrification in paddy soils.. This was done by extracting soil nirK gene from rice field at heading stage using specific primers and Illumina Miseq high-throughput sequencing technology. The results showed that CR significantly increased the contents of nitrate nitrogen, total nitrogen and total carbon in paddy soils at heading stage, but had no significant effect on the ratio of carbon to nitrogen, contents of available nitrogen and ammonium nitrogen in soil. Compared with MR, CR significantly increased nirK gene abundance in soil, but did not significantly change its diversity. CR treatment changed the composition of nirK gene micro-organisms in the levels of order, family, genus and species. Compared with MR, CR reduced all taxonomic groups. The analysis of relative abundance of order showed no significant difference between CR and MR treatments. CR treatment changed species order, but did not change the relative abundance of common orders. RDA analysis showed that CR significantly changed community structure of nirK gene in soil. Nitrate nitrogen content was the main factor affecting the community structure of nirK denitrifying bacteria. It was obvious that rice-crayfish farming system had no significant effect on microbial diversity, but significantly increased microbial abundance index. In addition, it changed nirK denitrifying microbial community structure in terms of order, family, genus and species.