Abstract: To evaluate the effects of ambient temperature and day-length respectively in setting metabolic compensation of mitochondria in juvenile of the southern catfish (Silurus meridionalis Chen), the organ index of the heart, kidney and liver and their state 3 rates of mitochondria and cytochrome C oxidase activity (CCO) were measured in the tested fishes at different acclimations. Two experimental groups were acclimated to high temperature (27.5℃) and low temperature (12.5℃) at equivalent photoperiod (12L:12D), and other two groups were kept at long day-length (16L:8D) and short day-length (8L:16D) condition at same moderate temperature (20℃). There were 24 individuals in each group. Fish were maintained at these acclimation conditions for 8 weeks before sampling. In condition of the equivalent photoperiod, the organ index of the heart, kidney, and liver in the cold-acclimatized group (12.5℃, 12L:12D) were all significantly higher than that in the warm group (12L:12D, 27.5℃) (P 0.05). The acclimation of day-length did not cause any change in organ mass at same moderate temperature. At assay temperature of 12.5, 20, and 27.5℃, both state 3 rates of mitochondria and activity of CCO in the heart, kidney, and liver in the short day-length group (8L:16D, 20℃) were significantly higher than those in long day-length group (16L:8D, 20℃). State 3 rates of mitochondria and activity of CCO in the three tissues were not influenced by thermal acclimation. The results showed that day-length initiates changes in the mitochondrial oxidative capacity and the temperature was the major ambient factor to alter the organ mass. It is suggested that during seasonal acclimatization photoperiod signal and thermal condition might have a cooperative effect on the adjustment for metabolic compensation in the southern catfish.