The emerging three-dimensional (3D) printing technique has shown prominent advantages to fabricate hydrogel-based tissue scaffolds for the regeneration of bone defects. Here, a tough polyion complex (PIC) hydrogel was synthesized, and multiwalled carbon nanotubes (MWCNTs) were incorporated into the PIC matrix to form the PIC/MWCNT biohybrid hydrogel, which was manufactured into 3D scaffolds by extrusion-based 3D printing for bone defect repair. To the best of our knowledge, this is the first study to combine CNTs with PIC hydrogels as biohybrid scaffolds for bone repair. The results from the in vitro cell culture demonstrated that the PIC/MWCNT scaffolds exhibited good biocompatibility with rat bone marrow-derived mesenchymal stem cells (rBMSCs) and facilitated the osteogenic differentiation of rBMSCs. Moreover, rBMSCs cultured on the PIC/MWCNT scaffolds exhibited a higher degree of osteogenic differentiation than those cultured on PIC scaffolds in terms of mineralized matrix formation and osteogenesis-related gene upregulation. The in vivo experiments in a calvarial defect model of Sprague-Dawley (SD) rats revealed that the PIC/MWCNT scaffolds significantly promoted the regeneration of calvarial defect healing. These findings suggest that the PIC hydrogel is a potential scaffold material for bone regeneration, and the addition of MWCNTs provides further enhancement in bone repair efficiency by the PIC/MWCNT scaffolds.