Osteoporosis has become an important risk factor for human health, although there has been some progress in the pathogenesis, diagnosis and treatment of osteoporosis, many problems remain to be solved. Metabolomics is an integral part of systems biology, the purpose of which is to find out the relationship between the metabolite changes and the physiological and pathological changes to reveale the pathogenesis of diseases and contribute to the diagnosis, treatment and prognosis evaluation of diseases by conducting quantitative analysis of metabolites in organisms. This paper reviews the basic technology of metabolomics and its application in pathogenesis, early diagnosis and treatment of osteoporosis.