Guided bone regeneration (GBR) is a frequently used technique for patients with insufficient alveolar bone. The discovery of bone substitutes that can enhance osteogenesis is critical for GBR. Graphdiyne (GDY), a newly discovered carbon-based nanomaterial, has been recognized as the most stable allotrope of acetylene carbon and is anticipated to be able to promote osteogenesis. Whereas it still remains unknown whether it could enhance osteogenic differentiation of bone marrow mesenchymal stem cells (BMSCs). In this study, GDY was modified with polyethylene glycol (PEG) and the influences of GDY-PEG at different concentrations on BMSCs cell growth and osteogenic differentiation were researched for the first time. In this study, we found that GDY-PEG at low concentration possessed premium bio-compatibility and revealed evident facilitation of BMSCs osteogenic differentiation. The cell growth and osteogenic differentiation of BMSCs treated with GDY-PEG were dose-dependent. GDY-PEG at 1 μg/mL demonstrated the optimal promoting effects of BMSCs osteogenic differentiation. Moreover, the regulating effect of BMSCs osteogenic differentiation by GDY-PEG might be associated with the Wnt/β-catenin signaling pathway. In all, the present study indicated a novel application of GDY in promoting bone tissue regeneration, providing a novel biomaterial for bone augmentation in clinics.