The purpose of this study was to elucidate the potential relationship between skeletal muscle mitochondrial function and bone health by analyzing the effect of training modality on body composition, physical performances, musculoskeletal mitochondrial function, and bone microstructure. 25 female 17-week-old C57BL/6 mice were randomly divided into CON (control, n=8), CT (combined training, n=8), HIIT (high intensity interval training, n=9) groups and underwent a 12-week training program. Measurement variables included body composition (weight and skeletal muscle mass), physical performance (grip strength, exhaustion test, Rota-rod test), skeletal muscle mitochondrial function (O₂ consumption, H₂O₂ emission, Ca++ retention), and the trabecular, cortical and whole bone microstructure in the right tibia. Both training groups attenuated weight gain compared to the control group (p=0.007), but there were no statistically significant differences in muscle mass (p>0.05). CT was more effective for strength improvement (p=0.001), while HIIT demonstrated greater effectiveness in enhancing aerobic endurance (p<0.001). For the mitochondrial functions, O₂ consumption and Ca++ retention did not show statistical significance, but HIIT exhibited significantly higher in H₂O₂ emission than CT (p<0.05). In terms of bone microstructure, both training increase trabecular bone parameters including bone volume fraction (BV/TV) (CT, p<0.001; HIIT, p<0.001), trabecular number (Tb.N) (CT, p=0.002; HIIT, p=0.001), and trabecular thickness (Tb.Th) (CT, p=0.01; HIIT, p=0.007) compared to CON, but no significant differences were observed in the cortical bone and whole bone (p>0.05). Furthermore, correlations were found between muscle strength and BV/TV (r=0.48), Tb.Th (r=0.411), as well as between aerobic endurance with all trabecular parameters (r=0.4 to 0.7). However, contrary to the hypothesis of this study, a positive correlation was observed between H₂O₂ emission and Tb.Th (r=0.514), cortical area (Ct.Ar, r=0.602), cortical perimeter (Ct.Pm, r=0.643), and polar moments of inertia (pMOI, r=0.637), and negative correlation between white gastrocnemius Ca++ retention with whole bone parameters (bone mineral content, BMC; bone mineral density, BMD; bone area, B.Area; bone volume, B.Volume) In conclusion, HIIT improve aerobic endurance, and may also enhance musculoskeletal O₂ consumption capacity more than CT. Also, HIIT improve bone health in the lower body, as well as CT. Therefore, HIIT is an effective exercise modality for improving O₂ consumption and bone health.