Abstract: The red swamp crayfish (Procambarus clarkii) is the most extensively farmed crustacean in China. The intestinal microbiota plays a crucial role in host physiological functions. However, it remains unclear whether there are differences in intestinal microbiota structure and function among different culture models of crayfish. In this study, we utilized Illumina MiSeq high-throughput sequencing technology to analyze the intestinal microbiota of crayfish under different cultivation models: rice-crayfish co-culture (RC), single-crayfish pond culture (SC), and mixed-crayfish pond culture (MC). We also analyzed water physicochemical factors and further explored the relationship between intestinal microbiota and physicochemical factors in the water. The results revealed that: Species composition analysis showed that at phylum level, the intestinal microbiota composition was consistent across three culture models, with Tenericutes, Proteobacteria, and Firmicutes as the absolute dominant groups. At genus level, there were some differences among different culture models, with Bacillus having the highest relative abundance in RC group, Lactococcus dominated in SC group, and Aeromonas was most abundant in MC group. Diversity analysis showed that the species richness and diversity of intestinal bacteria in group MC were the highest, and there were significant differences in the community structure of intestinal bacteria of crayfish under three culture models. Functional prediction showed that Vitamin Biosynthetic metabolic pathway was significantly enriched in RC group, while lactose degradation and galactose degradation metabolic pathways were prominent in SC group. In the MC group, pathways related to fatty acid and lipid degradation, CMP-pseudaminate biosynthesis, and superpathway of lipopolysaccharide biosynthesis metabolic pathways were significantly enriched. Network analysis showed that the cooperative relationship accounted for 83.76% of the interactions within the intestinal microbiota, with Erysipelotrichaceae and Sphingomonas bacteria were the main nodes of the network. Furthermore, the abundance of Lactobacillus in the gut was significantly positively correlated with TP concentration and negatively correlated with \rmNH^+_4 concentration in the water. In conclusion, the intestinal microbiota of crayfish includes core microbial groups mainly composed of Tenericutes, Proteobacteria and Firmicutes in the gut of crayfish, which remain stable across different culture models. However, there are notable variations in both community structure and metabolic function of intestinal bacteria among the three models. These findings enhance our understanding of crayfish intestinal microbiota and provide a theoretical basis for the screening of intestinal probiotics and their application in production practice.