Objective To explore the rice fields adaptive characteristics of golden back carp (Cyprinus carpio var. Jinbei) and the relationship between their gut and different rice fields environments.

Method The study focuses on the growth of goldenback carp in flat plate, “single” line ditch, and “cross”shaped ditch, using morphological, enzymatic and molecular biological methods were used to investigate the effects of adding ditches and pits in rice fields on the intestinal structure, digestive enzyme activities and microbial communities of the goldenback carp.

Result The villus width of goldenback carp intestine in “cross”shaped ditch group was the widest (173.59 μm), followed by the “single” line ditch group (157.72 μm), and the lowest was the flat plate group (139.69 μm). The trypsin activity of the “cross-shaped ditch” group and the “single line ditch” group were 4 662.65 and 4 676.12 U·gprot⁻¹, respectively, significantly higher than that of the flat plate group (3 752.34 U·gprot⁻¹) (P < 0.05). At the phylum level, after adding ditches and pits in rice fields, the Proteobacteria and Firmicutes remained dominant, but the Actinobacteria replaced the Bacteroidetes as the dominant phylum. .At the genus level, the dominant genera in the flat plate group were Streptococcus, Janthinobacterium, and Pseudomonas. There were significant changes in the dominant genera of the “single” line ditch and “cross”shaped ditch groups, among the top three dominant bacterial genera in each group, one dominant bacterial genus changed in the“single” line ditch, and two dominant bacterial genera changed in the “cross”shaped ditch.

Conclusion The intestinal structure, digestive enzyme activity, microbial community, and dominant bacterial groups of the goldenback carp would change with the addition of ditches and pits in rice fields, regulating metabolism to adapt to the new rice field water environment. Despite the changes, the composition of the core intestinal flora of the goldenback carp remained relatively stable.