Efficient bone reconstruction, especially of the critical size after bone damage, remains a challenge in the clinic. Bone marrow mesenchymal stem cell (BMSC) osteogenic differentiation is considered as a promising strategy for bone repair. Nicotinamide adenine dinucleotide (NAD+) regulating BMSC fate and cellular function enhance osteogenesis, but is hardly delivered and lack of targeting. Herein, a novel and biocompatible scaffold was fabricated to locally deliver a precursor of NAD+, nicotinamide mononucleotide (NMN) to the bone defect site, and its bone repair capability and healing mechanism were clarified. NMN-based hyaluronic acid methacryloyl hybrid hydrogel scaffold (denoted as NMN/HAMA) was prepared via photopolymerization. In vitro RT-qPCR analysis, western blotting, Elisa and alizarin red S staining assays demonstrated that the NMN/HAMA hybrid hydrogel regulated BMSCs cellular function in favour of osteogenic differentiation and mineralization by upregulating the mRNA and proteins expression of the osteogenic genes type I pro-collagen (Col-1), bone morphogenic protein 4 (BMP4), and runt-related transcription factor 2 (RUNX2) via the SIRT1 pathway. Implantation of such hybrid hydrogels significantly enhanced bone regeneration in rodent critical calvarial defect models. Furthermore, restoration of the bone defect with NMN administration was inhibited in Prx1 Cre+; SIRT1flox/flox mice, confirming that the NMN/HAMA hybrid hydrogel scaffold promoted bone regeneration via the SIRT1-RUNX2 pathway. These results imply that NMN-based scaffold may be a promising and economic strategy for the treatment of bone defects.