Simple Summary: In order to investigate the effects of low oxygen stress on the survival rate, antioxidant, anaerobic metabolic enzymes, and related genes of crayfish during aquaculture. This experiment conducted a 24-h low oxygen stress experiment on juvenile and subadult crayfish, and the results showed that the higher the degree of low oxygen stress, the higher the antioxidant and anaerobic metabolic enzyme activity and gene expression levels of juvenile crayfish and subadult crayfish. Compared with subadult crayfish, the antioxidant system of crayfish larvae is more sensitive to hypoxic environments. The red swamp crayfish Procambarus clarkii is the most reared shrimp in China, but it is often affected by hypoxia stress in the process of seedling culture and adult crayfish culture. The oxygen consumption rate and asphyxiation point of juvenile crayfish (1.17 ± 0.03 g) and subadult crayfish (11.68 ± 0.11 g) at different temperatures (20, 22, 24, 26, and 28 °C) were studied. The survival, glycolysis, and expression of antioxidant genes were compared under 24 h acute hypoxia stress (1, 2, and 3 mg/L) and normal dissolved oxygen (7.5 mg/L). The results showed that the oxygen consumption rate and asphyxiation point of juvenile and subadult crayfish increased with increasing temperatures (20–28 °C). At the same temperature, the oxygen consumption rate and asphyxiation point of juvenile crayfish were significantly higher than those of subadult crayfish (p < 0.05). Within 24 h, the three hypoxia stress environments did not lead to the death of crayfish, indicating that P. clarkii has a strong ability to adapt to hypoxia. Hypoxia stress significantly affected the activities of antioxidant and anaerobic metabolic enzymes and gene expression in juvenile and subadult crayfish. The activities of the superoxide dismutase (SOD), catalase (CAT), and lactate dehydrogenase (LDH) and the content of lactic acid (LD) in the hepatopancreas of juvenile and subadult crayfish in the hypoxia stress groups increased significantly. The expression levels of SOD mRNA, CAT mRNA, Hsp70 mRNA, and crustin 4 mRNA in the hepatopancreas of juvenile and subadult crayfish in the hypoxia stress groups were significantly higher than those in the control group (p < 0.05), and the higher the degree of hypoxia stress, the higher the expression of each gene. The results showed that the antioxidant system of juvenile crayfish was more sensitive to hypoxia environments, and hypoxia stress resulted in increased stress levels in juvenile crayfish and subadult crayfish. [ABSTRACT FROM AUTHOR]