Simple Summary: Pseudobagrus ussuriensis is a high-value fish species widely distributed in various river basins across China. Its benthic lifestyle and lack of scales make its skin susceptible to damage, leading to diseases and mortality. Hypoxia represents a significant factor affecting fish health, whether in captive environments or natural water bodies. Exposure to low oxygen levels can result in various adverse effects, including causing an immune response in fish. In this study, we aimed to elucidate the differential immune responses of distinct tissues to acute hypoxia and reoxygenation by analyzing the histophysiological and transcriptional changes in the brain and skin of P. ussuriensis. Our findings revealed that both the brain and skin exhibited immune responses to hypoxia, which persisted even after reoxygenation. However, it was observed that the overall immune response intensity in the brain was lower than that in the skin. This research provides novel insights into the molecular mechanisms underlying the response of P. ussuriensis to hypoxia stress. Pseudobagrus ussuriensis is an unscaled fish that is more susceptible to skin damage than scaled fish. To investigate the impacts of hypoxia and reoxygenation on skin and brain immunity, juvenile P. ussuriensis were subjected to hypoxia conditions (DO: 0.8 ± 0.05 mg/L) for durations of 0, 3, 6, and 12 h, followed by 12 h of reoxygenation (DO > 6 mg/L). Histological analysis showed a significant increase in the number of skin mucosal cells after 12 h of hypoxia and a significant decrease after 12 h of reoxygenation when compared to the control group. As the duration of hypoxia increased, an increase in antioxidant (SOD, CAT, GSH, MDA) and immune (cortisol, LZM) physiological parameters of the skin and brain appeared. The results of transcriptomic studies showed that the number of differential genes was greater in skin than in brain. Most of the immune pathways in both tissues under hypoxia conditions were all nonspecific immunity (TNF, IL-17, chemokines), while both tissues maintained their homeostasis through active energy supply and cell cycle regulation. Meanwhile, both physiological parameters and RNA transcriptome results showed that 12 h of reoxygenation could not completely eliminate the negative effects of 12 h of hypoxia. This study offers new insights into the immune responses of P. ussuriensis skin and brain during acute hypoxia and reoxygenation. [ABSTRACT FROM AUTHOR]