Bone defect repair is one of the most common issues in clinic. Developmental multifunctional scaffolds have become a promising strategy to effectively promote bone defect repair. Here, a series of multifunctional hydrogels that integrate stable mechanical properties, non-swelling property, conductivity, and photothermal antibacterial properties were developed based on gelatin methacrylate (GM), acryloyl-β-cyclodextrin (Ac-CD), and β-cyclodextrin (β-CD)-functionalized reduced graphene oxide (rGO) for skull defect regeneration. Ac-CD was added as a host macromolecule to improve the toughness of the hydrogels. rGO was selected as the conductive element to endow the hydrogel with conductive properties, and the β-CD unit in rGO allowed rGO to interact with GM to improve the dispersity of rGO. In vitro/in vivo studies confirmed that the GM/Ac-CD/rGO hydrogel had good biocompatibility and simultaneously promoted the proliferation and osteogenic differentiation of MC3T3-E1 cells, and further accelerated in vivo bone defect repair in a rat skull defect model. Moreover, two-photon laser scanning microscopy (TPLSM) was used for the first time to evaluate bone defect repair by exploring the collagen and mineralized structure directly in bone defect specimens. In short, these multifunctional hydrogels have shown promising applications in bone tissue formation and further accelerate bone defect repair, indicating their great potential for clinical application.