This experiment studied the changes in serum biochemical characteristics, intestinal microstructure, intestinal microbial flora diversity, and species abundance of carp under the conditions of rice fields.In Liannan Yao Autonomous County from June to August 2019, paddy fields and ponds were selected, and carp juveniles of the same size were stocked for 3 months without feeding. After the test, sampling and testing were performed uniformly. The results showed that paddy field environment significantly incresased the body length and weight of the carp, significantly reduced the carp serum alanine aminotransferase(ALT) activity and intestinal microvilli height (P<0.05); the content of serum complements C3 and C4 showed an upward trend, but there was no significant difference (P>0.05). In terms of intestinal microorganisms, the environment significantly increased the diversity of carp intestinal flora, and significantly increased the abundance of Verrucomicrobia and Proteobacteria at the phylum level (P<0.05), significantly reducing the abundance of Fusobacteria (P<0.05); At the genus level, the abundance of Cetobacterium, Plesiomonas, Bacteroides and Aeromonas was significantly reduced (P<0.05). The experimental results confirmed that the paddy environment changed the intestinal microbial diversity and the abundance of functional genes related to metabolic capacity, reduced the abundance of some conditional pathogens, reduced the probability of disease outbreaks, and helped to maintain liver function stability.