It is important to study the effect of flow rate on the swimming movement of juvenile Thamnaconus septentrionalis. In this experiment, a self-made swimming device was used to study the swimming ability and behavior of juvenile fishes at different body weights (10, 15, 20, and 25 g) and different temperatures (12, 16, 20, 24, and 28℃), and to investigate the metabolism of juvenile fishes at the flow rates of 0.12, 0.24, 0.36 and 0.48 m/s at any time. The results show: The critical swimming speed (UC) of the four sizes were 0.42±0.03, 0.47±0.01, 0.53±0.03, and 0.62±0.01m/s, respectively. Burst swimming velocity (UB) was 0.53±0.06, 0.56±0.02, 0.60±0.02 and 0.72±0.01 m/s, respectively. The swimming ability of juvenile UC and UB was significantly improved with the increase in body mass. The UC and UB of juvenile fish at 25 g at five temperature groups increased and then decreased with the increase of temperature, and reached the maximum value at 24℃, which was significantly different from that of other groups (P < 0.05). The oscillation frequency of the caudal fin, dorsal fin, and anal fin increased with the increase in flow velocity, and the oscillation frequency of the caudal fin was significantly different among the four flow velocity groups (P < 0.05). The oscillation frequency of the dorsal fin and anal fin was higher than that of the caudal fin, and there was no significant difference between the adjacent dorsal fin and anal fin in the 0.24-0.48 m/s group. The trend rate with flow velocity was significantly higher than that with static water, and there was no significant difference among flow velocity groups. Juvenile fish at a flow rate of 0.36 m/s and 0.48 m/s for a long time will increase the consumption of glycogen and blood sugar in vivo and show anaerobic metabolism. Studies show that juvenile Thamnaconus septentrionalis has strong swimming ability, and it is necessary to control the instantaneous current not to exceed UB and not to be in UC for a long time. From the perspective of metabolism, lactic acid accumulation will cause harm to fish. Thus, juvenile fish should not be in a flow rate higher than 0.36m/s for a long time in the breeding process and the flow rate of the water should be adjusted regarding the water temperature and fish specifications