Organisms at all levels of evolutionary complexity react to hypoxic stress. To clarify the effects of acute hypoxia on physiological and biochemical responses of Larimichthys crocea, we measured the activity levels of the antioxidant enzymes superoxide dismutase and catalase, hemoglobin concentration, functional indices of the liver (aspartate transaminase, alanine transaminase), heart (phosphocreatine kinase), and immune system (alkaline phosphatase), as well as mRNA expression levels of the immunity-related genes Hsp70 and HIF-1α at different time points of hypoxic. In addition, liver, gill, and kidney samples were histologically analyzed. We found that hemoglobin concentration and all enzyme activities increased during hypoxia, although these effects were transient and most indices returned to basal levels thereafter. The extent of the increase in the parameter values was inversely proportional to the dissolved oxygen content. Hsp70 and HIF-1α mRNA expression levels increased significantly in the blood, liver, gills, and kidneys following exposure to hypoxia, which may play an important role in protecting fish against oxidative damage. However, we found histological evidence of hypoxia-induced injuries to the gills, liver, and kidneys, which are involved in breathing, detoxification, and osmotic balance maintenance, respectively. Thus, despite the upregulation of defensive mechanisms, acute hypoxia still caused irreversible damage of organs. In conclusion, we observed that, in response to acute hypoxic stress, L. crocea enhances immune defensive function and antioxidant capacity. A better understanding of the regulation of the molecular anti-hypoxia mechanisms can help speeding up the selective breeding of hypoxia-tolerant L. crocea.