Excessive buildup of endogenous glucocorticoids has been closely linked to postmenopausal osteoporosis (PMOP), though the underlying mechanisms remain unclear. This study examines the role of glucocorticoid receptor (GR) signaling in PMOP, particularly its translocation to mitochondria, interaction with the peripheral benzodiazepine receptor (PBR), and impact on bone formation. In vitro, primary bone marrow mesenchymal stem cells (BMSCs) from mice were cultured to induce osteogenesis under varying concentrations of dexamethasone. Nuclear GR, mitochondrial GR, and PBR levels were measured, along with the effects of Importazole, an importin-β inhibitor, and Emapunil, a PBR inhibitor, on osteogenic differentiation. In vivo, ovariectomized mice were treated with Importazole and Emapunil to assess their anti-osteoporotic potential. Our results indicate that ovariectomized mice displayed increased nuclear GR, decreased mitochondrial GR, and elevated PBR expression in BMSCs. High dexamethasone impaired osteogenic differentiation, characterized by nuclear GR accumulation, reduced mitochondrial translocation, and increased PBR expression. Co-immunoprecipitation confirmed a direct interaction between mitochondrial GR and PBR. Importazole reduced nuclear GR levels, promoting bone formation and alleviating osteoporosis, while Emapunil enhanced GR mitochondrial translocation, improved mitochondrial function, and strengthened bone health. Combined, Importazole and Emapunil showed superior anti-osteoporotic effects compared to either treatment alone. These findings suggest that estrogen deficiency promotes nuclear GR accumulation and PBR expression in BMSCs, limiting GR mitochondrial translocation and reducing osteogenic differentiation. Combining Importazole and Emapunil could mitigate these effects, offering a promising therapeutic strategy for PMOP.