Most osteoporosis (OP) fracture accidents in men are not only due to low BMD but also because of unhealthy muscle support. However, it has been a limited number of reports about how muscle metabolism is disturbed by OP in male patients. In this work, pathway analysis based on metabolomic research was carried out to fill this gap. Classical orchiectomy procedure was adapted to create OP animal model. Micro-CT and pathological section were applied for bone and muscle phenotype assessment and pathology analysis. UPLC-Q-TOF/MS and UPLC-QQQ-MS/MS were applied to measure metabolites in skeletal muscle samples among groups. In total, 31 significantly differential metabolites were detected by comparing between healthy model and OP animals, and 7 representative metabolites among the 31 significantly differential metabolites were identified and validated experimentally by UPLC-QQQ-MS/MS (xanthine, L-phenylalanine, choline, hypoxanthine, L-tryptophan, succinic acid, and L-tyrosine). Ingenuity Pathway Analysis analysis revealed significantly enriched pathways involved in inflammatory, oxidative stress, and necrosis. To our best knowledge, this is the first study that investigated early muscle disorder processes in OP cases at metabolic level, which facilitate early intervention and protection from OP fracture for aged men.