The hypogeomagnetic field (HMF) is one of the key risk factors for manned deep space missions. It has been reported that HMF exposure affects multiple exercise-related behaviors of animals, but the long-term effects of HMF on the exercise capacity of adult humans needs further investigation to determine the potential risk of HMF exposure during deep space missions. In this study, we reared adult male C57BL/6 mice in an HMF for one month, simulated by a 3-axis Helmholtz coil system, and examined the effects on their exercise capacities at behavioral, tissue, cellular, and molecular levels. Compared with that of the control mice reared in the geomagnetic field, the endurance of the HMF-exposed mice was significantly reduced. Decreases were also observed in the citric acid level and the number of subsarcolemmal mitochondria in skeletal muscles, and morphological alterations of skeletal mitochondria were noted. These results indicate an HMF-induced inhibition of muscular mitochondrial function and an endurance-related decline in the process of energy metabolism. Our findings provide direct in vivo evidence to demonstrate that mitochondria can respond to HMF exposure and that mitochondrion-related indices could be used for risk evaluation and the development of methods of counteraction.