Abstract: 【Objective】 This study aimed to investigate the effects of different integrated rice-fish farming modes on intestinal microenvironment and digestive functions of two carp species， providing reference for selective breeding improvement of new strains of red FFRC No. 2. 【Method】 Using FFRC No. 2 and red FFRC No. 2 as experimental objects， four treatment groups were established： FFRC No. 2 without feeding （B-F）， red FFRC No. 2 without feeding （B-R）， FFRC No. 2 with feeding （T-F）， and red FFRC No. 2 with feeding （T-R）. A comparative culture trial of 49 d was conducted. The microbial community structures in water samples， soil samples， and intestinal content samples were analyzed using 16S rRNA sequencing， and a comprehensive evaluation was performed by combining intestinal tissue sections with digestive enzyme activity tests. 【Result】 The final body mass and final body length of the T-R group were significantly higher than those of the B-F group （P<0.05， the same below）. In the four groups， microbial community richness and species diversity followed the order of soil samples > water samples > intestinal content samples. The similarity between soil samples and water samples was relatively high， and they first clustered into one group， and then clustered with intestinal content samples. The Proteobacteria maintained a relatively high relative abundance in the soil samples， water samples， and intestinal content samples of the four groups. In the T-R group， the genus with the highest relative abundance was Cetobacterium， followed by Polynucleobacter， Aeromonas， unclassified genera， and Rhodoferax. The T-R group exhibi-ted the greatest intestinal villus height. In the B-R and T-R groups， the villus height was uniform and neatly arranged， whereas obvious differences in intestinal villus height were observed between the B-F and T-F groups. The numbers of intestinal goblet cells in the T-F and T-R groups were higher than those in the B-F and B-R groups respectively. For both carp species， amylase activity in the feeding groups was lower than that in the non-feeding groups， lipase activity was significantly higher than that in the non-feeding groups， and trypsin activity was higher than that in the non-feeding groups. 【Conclusion】 The colonization of dominant intestinal microbial communities in fish under different integrated rice-fish farming systems is primarily influenced by host genetic background， with feeding playing only a modifying role. The diversity of beneficial intestinal microbial communities， structural integrity of tissues， and digestive functions exhibit positive synergy， constituting an intrinsic mechanism for evaluating fish environmental adaptability. In this synergistic system， the red FFRC No. 2 displays stable germplasm superiority and has developed adaptive characteristics to paddy field culture.