Abstract: At present, the research on environmental stress of fish intestinal tissues has attracted the attention of scholars. In order to explore the effects of hypoxia (1.0±0.1) mg/L and recovery (7.0±0.5) mg/L on the intestinal tissues of hybrid yellow catfish “Huangyou-1”, the changes of intestinal oxidative stress index, histological morphology, cell apoptosis and microbial composition were analyzed by enzyme activity determination and H & E staining, qRT-PCR, TUNEL detection and 16S rRNA sequencing technology. The results showed that: (1) Antioxidant enzyme activities (SOD, CAT, GSH-Px), energy metabolism enzyme activity (LDH), malondialdehyde (MDA) and lipid peroxide (LPO) of intestine increased significantly under hypoxia stress, and the oxidative stress reaction was also severe after the recovery of dissolved oxygen. (2) After hypoxia stress, the intestinal tissue damage gradually intensified, the goblet cells were swelled and the mucosal layer was eroded. The physiological changes caused by hypoxia were not significantly improved after 24h oxygen recovery. (3) The degree of intestinal cell apoptosis intensified with the prolongation of hypoxia, and the expression levels of apoptosis-related genes (bax, caspase9 and p53) increased significantly, while the mRNA expression levels of bcl-2 decreased. (4) The relative abundance of intestinal microbes were reduced in the hypoxic stress stage. Among 72h hypoxic stress, Firmicutes (47.8%) and Bacteroidetes (40.6%) had the most dominant abundances, and the number of intestinal flora increased after the recovery of dissolved oxygen, KEGG function prediction showed that most of the intestinal microbes were related to metabolic pathways. The research results can provide a theoretical basis for analyzing the physiological regulation mechanism of hybrid yellow catfish “Huangyou-1” in response to hypoxia stress and recovery.