In order to study the physiological responses of hybrid Pelteobagrus fulvidraco (Pelteobagrus fulvidraco ♀ × Pelteobagrus vachelli ♂) under different dissolved oxygen (DO), the experiment analysed and compared the changes in growth, oxidative stress, apoptosis, and intestinal microorganisms of hybrid P. fulvidraco exposed to DO in group L (DO = 6.0 ± 1 mg/L), group M (DO = 9.0 ± 1 mg/L, as a control group in this study) and group H (DO = 12.0 ± 1 mg/L) for 7 days, 14 days, and 14 days of restoration of DO. The results showed that the growth were inhibited in groups L and H, and the activities of antioxidant enzymes (superoxide dismutase, catalase, malondialdehyde, and glutathione) in gill and liver were differently altered in group L and H compared to group M. It was found that there was fusion of gill lamellae in group H, and there was basal proliferation in group L. At the same time, both H and L groups exhibited inflammatory reactions, cell necrosis, and vacuoles in liver. Morphometric analysis showed that groups H and L exacerbated gill apoptosis, while the liver showed no significant changes among different treatments. After different DO treatments, a significant decrease in the diversity and richness of intestinal microorganisms in the H and L groups compare to M group. After 14 days of treatment with oxygen concentration restored to 9 mg/L, oxidative stress, gill and liver damage were alleviated, and the diversity and richness of intestinal microorganisms significantly increased. In addition, the contribution of water column microorganisms to intestinal microorganisms was elevated to 20.1% with increasing oxygen concentrations. These results suggest that DO fluctuation affects the physiological functions of hybrid P. fulvidraco and negatively affects the healthy culture of the fish.