Ethnopharmacological relevance: Dipsacus asper Wall. ex C.B. Clarke (DA) is an effectively traditional Chinese medicine for treating osteoporosis and bone fracture. Until now, studies on pharmacological mechanism of DA mostly centered on cell and gene level, little is known about its metabolic signatures. The aim of this study is to investigate the anti-osteoporosis effects of crude and wine-processed DA by global and untargeted metabolic profiling of rats serum, liver and kidney derived from sham, model and treated groups. Method: A total of 25 female Wistar rats were divided into five groups: sham group, model group, E2, crude and wine-processed DA treated group. The treatment rats were orally administered 17 beta-estradiol, crude and wine-processed DA extract at a therapeutic dose once daily throughout the experimental period, while sham group and model group were orally gavaged approximately volume of saline solution. After 16 weeks, all serum, liver and kidney samples of five groups were collected and their metabolomic alterations were monitored by gas chromatography mass spectrometry (GC MS). The resulting dataset was analyzed by principal component analysis (PCA) and partial least squares discriminant analysis (PIS-DA). The identification of all potential biomarkers was performed using reference standard or NIST library. Moreover, clinical chemistry and biomechanical analysis were also performed to ensure the success of the osteoporosis model and to validate the anti-osteoporosis effect of crude and wine-processed DA. Results: Clear separation trend among sham, model and treatment group was observed in PCA score plot. The anti-osteoporosis effect of DA and wine-processed DA can be indicated in PLS-DA score plots. A total of 80 and 74 metabolite biomarkers were identified for DA and wine-processed DA treated groups, respectively. Pathway analysis revealed that phenylalanine, tyrosine and tryptophan biosynthesis, valine, leucine and isoleucine biosynthesis, methane metabolism, glycine, serine and threonine metabolism, galactose metabolism were the major intervened pathways. Compared with model group, levels of all biomarkers were gradually restored to normal after administration of DA and wine-processed DA. Conclusion: The anti-osteoporosis effect of DA and wine-processed DA has been reliably confirmed by the metabolomics approach. The osteoporosis might be prevented by DA and wine-processed DA via intervening amino acid metabolism, carbohydrate metabolism and energy metabolism in vivo in rats.