The phenomenon of oxygen deficiency is common in intensive aquaculture and live fish transportation, and has become an increasingly important issue in the aquaculture industry. The effects of hypoxic stress on water quality, biochemical parameters, and tissue structure during the transport of Siberian hybrid sturgeon (♀Acipenser baerii × ♂Acipenser schrenckii) larvae were investigated. The hybrid sturgeon larvae were placed in environments with dissolved oxygen concentrations of 2.5 ± 0.5 mg/L and 7.5 ± 0.5 mg/L for simulated transportation. Sampling was conducted before transport (0 h) and at 3, 6, 9, and 12 hours post-transport. The results showed that after 12 hours of transport, the survival rate of larvae in the hypoxic group was 54%. The serum cortisol (COR) concentration, liver alkaline phosphatase (AKP) and acid phosphatase (ACP) activities were significantly higher than those before transport (P<0.05). Serum glucose (GLU) levels peaked at 6 hours post-transport. Liver malondialdehyde (MDA), glutathione (GSH) content, and superoxide dismutase (SOD) activity were significantly higher than those in the normoxic control group (P<0.05). The liver antioxidant capacity (T-AOC) and lysozyme (LZM) activity in the hypoxic group exhibited a trend of initial decrease followed by an increase. After 12 hours of transport, the muscle glycogen content in the hypoxic group was significantly lower than that in the normoxic control group (P<0.05), while lactic acid levels peaked at 3 hours. More severe tissue damage was observed in the liver of hypoxic group larvae after 12 hours of transport. The study indicates that hypoxic stress during transportation affects juvenile fish survival rates, water quality, and other parameters, leading to oxidative stress responses and exacerbating liver tissue damage.