Abstract: Yellow catfish is a high-quality and popular fish that is widely grown in freshwater farms. The rice-fish co-culture systems in Hani Terrace is a new agricultural model. To explore the differences of intestinal microbiota of hybrid yellow catfish (Tachysurus fulvidraco♀×Pseudobagrus vachellii♂) between rice-fish co-culture system (DY group) and traditional pond system (CT group), we conducted feeding experiment in terraces and ponds at an altitude of 634 meters in Honghe Hani Autonomous Prefecture of Yunnan Province. The 16S rRNA gene profiling analysis showed that the dominant flora of yellow catfish were Proteobacteria, Firmicutes, Bacteroidetes and Fusobacteria. Different culture patterns did not change the dominant microflora of yellow catfish, but affected the relative abundance of dominant flora. Compared with the CT group, the DY group had more abundance of Firmicutes and Bacteroidetes and less Proteobacteria at phylum level. At genus level, compared with DY group, the CT group had significantly increased abundance of Plesiomonas and significantly decreased abundance of genera Clostridium_sensu_stricto_1, Romboutsia, Paludibacter, Epulopiscium, and Bacteroides. Different culture patterns did not significantly affect the intestinal microbial richness of yellow catfish, but DY group had higher microbial evenness. Moreover, gram_negative and facultatively anaerobic microorganisms were enriched in CT group, and gram_positive and anaerobic microorganisms were enriched in DY group. In addition, gene related to biofilm forming and potential_pathogenicity were depleted in the DY group. These results indicate that DY group had higher intestinal microbial diversity, better stability and stronger resistance to diseases. The rice-fish co-culture system can provide a better living environment for yellow catfish.