BACKGROUND: Obesity and osteoporosis frequently coexist, and might have a causal relationship. Gut microbiota, associated with both lipid and bone metabolism, plays an important role in the pathogenesis of excessive fat accumulation and bone loss. The improvement of intestinal flora by prebiotics was a promising strategy for ameliorating obesity-related bone loss. METHODS: Obesity model was established by feeding mice with high fat diet (HFD) for 16 weeks. Fructooligosaccharides (FOS) and/or galactooligosaccharides (GOS) were daily gavaged to mice. Osteoblastic, adipocytic, and osteoclastic differentiation was performed on primary cells isolated from experimental mice. The composition of gut flora was evaluated by 16s rDNA sequencing. Expression of intestinal junction proteins was assessed by qPCR and immunohistochemistry. Cytokine levels were measured by qPCR. RESULTS: Long-term HFD caused decreased bone mass in mice, which was associated with decreased osteogenesis, increased osteoclastogenesis, and excessive adipogenesis. FOS/GOS treatment significantly alleviated HFD-induced bone loss and reversed the imbalanced differentiation of osteoblasts, adipocytes, and osteoclasts. In addition, our study showed that FOS/GOS administration ameliorated microbiota dysbiosis (manifested as enhanced Firmicutes:Bacteriodetes ratio and reduced biodiversity), downregulated expression of intestinal junction proteins (including Claudin1, Claudin15, ZO-1, and JAM-A), and increased inflammatory cytokines (including TNFα, IL6, and IL17) in HFD-fed mice. CONCLUSION: Long-term HFD led to decreased bone mass, with microbiota dysbiosis, leaky gut, and systemic inflammation. The administration of FOS/GOS could significantly increase biodiversity and SCFA concentrations of intestinal flora in HFD fed mice, then reverse high gut permeability and inflammatory cytokines, in the end protect against HFD induced osteopenia.