Objective To study the effects of different hypoxic training modes on the activities of respiratory chain complexes in the brain mitochondria of rats. Methods Forty healthy two-month-old male Wister rats were randomly divided into 5 groups: living low-training low(LoLo), living high-training high(HiHi), living high-training low (HiLo), living low-training high(LoHi), and living high-exercise high-training low(HiHiLo). Rats were forced to complete a 5-week endurance training program. All training sessions were performed at the same relative intensity under normoxic(P=632mmHg, simulating about 1500m altitude) or hypoxic conditions(P=493mmHg, simulating 3500m altitude) for each of the five groups, respectively. Mitochondria were isolated with differential centrifugation. Spectrophotometric analysis was applied to evaluate RCC (Ⅰ- Ⅲ) activities in brain mitochondria. Results Compared with the LoLo, brain RCC activities in C Ⅱ in rats from LoHi significantly decrease(P<0.05). Brain RCC activities in C Ⅲ in rats from HiHi, HiLo and LoHi significantly decrease and from HiHiLo significantly increase (P<0.01). Conclusion These findings suggest that among different altitude training modes, HiHiLo is the superior one in developing function of mitochondria respiratory chain of rat brain tissues.