Introduction: Musculoskeletal system gradually degenerates with aging, and a hypoxia environment at a high altitude may accelerate this process. However, the comprehensive effects of high-altitude environments on bones and muscles remain unclear. This study aims to compare the differences in bones and muscles at different altitudes, and to explore the mechanism and influencing factors of the high-altitude environment on the skeletal muscle system. Methods: This is a prospective, multicenter, cohort study, which will recruit a total of 4000 participants over 50 years from 12 research centers with different altitudes (50m-3500m). The study will consist of a baseline assessment and a 5-year follow-up. Participants will undergo assessments of demographic information, anthropomorphic measures, self-reported questionnaires, handgrip muscle strength assessment (HGS), short physical performance battery (SPPB), blood sample analysis, and imaging assessments (OCT and/or DXA, US) within a time frame of 3 days after inclusion. A 5-year follow-up will be conducted to evaluate the changes in muscle size, density, and fat infiltration in different muscles; the muscle function impairment; the decrease in BMD; and the osteoporotic fracture incidence. Statistical analyses will be used to compare the research results between different altitudes. Multiple linear, logistic regression and classification tree analyses will be conducted to calculate the effects of various factors (e.g., altitude, age, and physical activity) on the skeletal muscle system in a high-altitude environment. Finally, a provisional cut-off point for the diagnosis of sarcopenia in adults at different altitudes will be calculated. Ethics and dissemination: The study has been approved by the institutional research ethics committee of each study center (main center number: KHLL2021-KY056). Results will be disseminated through scientific conferences and peer-reviewed publications, as well as meetings with stakeholders.