Abstract: 【Objective】 To elucidate the causes of stunted growth in Cyprinus carpio rubrofuscus from the perspective of intestinal health，which provided theoretical reference for further investigation of the intrinsic relationship between the fish stunted growth and intestinal health. 【Method】 C. carpio rubrofuscus juveniles bred in the same batch in the same year were cultured in 2 culture modes for 5 months：recirculating water system and pond netting. They were then divided into 4 groups according to their body weight，with the following designations：normal group in recirculating water system （R-N）；growth-stunted group in recirculating water system（R-GS）；normal group in pond netting（P-N）；growth-stunted group in pond netting（P-GS）. The differences in intestinal tissue morphology，digestive enzyme activities and bacterial flora structure of C. carpio rubrofuscus among the 4 groups were compared and analyzed. 【Result】 In the 2 culture modes， the height of intestinal villi and the thickness of muscularis propria of growth-stunted C. carpio rubrofuscus were significantly lower than those of normal C. carpio rubrofuscus（P<0.05，the same below），and the activities of intestinal amylase，trypsin and lipase were lower than those of normal C. carpio rubrofuscus，with the difference in the activity of trypsin reaching a significant level. The Alpha diversity of the intestinal flora of C. carpio rubrofuscus in the pond netting mode was significantly higher than that of C. carpio rubrofuscus in the recirculating water system mode；however，the difference in the Alpha diversity of intestinal flora of growth-stunted and normal-growing C. carpio rubrofuscus in the same culture mode was not significant（P>0.05，the same below）. Compared with the normal-growing C. carpio rubrofuscus，the relative abundance of growth-stunted C. carpio rubrofuscus intestinal Proteobacteria was significantly decreased in the recirculating water system mode，while the relative abundance of Desulfobacterota，Firmicutes and Actinobacteria were significantly increased；the relative abundance of growth-stunted C. carpio rubrofuscus intestinal Fusobacteria and Firmicutes in the pond netting mode was significantly decreased，while the relative abundance of Chloroflexi，Cyanobacteria and Acidobacteria were significantly increased，and Desulfobacterota，Actinobacteria，Planctomycetes and Protebacteria also increased in relative abundance，but the differences were not significant. At the genus level，the relative abundance of unclassified Desulfovibrionaceae，Rhodococcus，Vibrio，Shewanella in the intestine of growth-stunted C. carpio rubrofuscus in the recirculating water system mode was significantly increased compared with that of normal C. carpio rubrofuscus；the relative abundance of unclassified Pirellulaceae and Fimbriiglobus in the intestine of growth-stunted C. carpio rubrofuscus in the pond netting mode was significantly increased compared with that of normal C. carpio rubrofuscus. The results of KEGG signaling pathway analysis showed that intestinal abundance differential flora in 2 modes of culture in growth-stunted and normal C. carpio rubrofuscus all enriched in the endocrine system pathway. 【Conclusion】 Both in the pond netting and recirculating water system modes，the intestinal health indexes of growth-stunted C. carpio rubrofuscus change greatly，which is manifested by the reduced activity of digestive enzymes and weakened ability to digest food. In other words，the reduced level of intestinal health is one of the main reasons for the differentiation of growth-stunted C. carpio rubrofuscus.