Reconstruction of critical sized bone defects in the oral and maxillofacial region continues to be clinically challenging despite the significant development of osteo-regenerative materials. Among 3D biomaterials, hydrogels and hydrogel composites have been explored for bone regeneration, however, their inferior clinical performance in comparison to autografts is mainly attributed to variable rates of degradation and lack of vascularization. In this study, we report hydrogel composite magnetic scaffolds formed from calcium carbonate, poly(vinyl alcohol) (PVA), and magnetic nanoparticles (MNPs), using PVA as matrix and calcium carbonate particles in vaterite phase as filler, to enhance the cross-linking of matrix and porosity with MNPs that can target and regulate cell signaling pathways to control cell behavior and improve the osteogenic and angiogenic potential. The physical and mechanical properties were evaluated, and cytocompatibility was investigated by culturing human osteoblast-like cells onto the scaffolds. The vaterite phase due to its higher solubility in comparison to calcium phosphates, combined with the freezing-thawing process of PVA, yielded porous scaffolds that exhibited adequate thermal stability, favorable water-absorbing capacity, excellent mineralization ability, and cytocompatibility. An increasing concentration from 1, 3, and 6 wt % MNPs in the scaffolds showed a statistically significant increase in compressive strength and modulus of the dry specimens that exhibited brittle fracture. However, the hydrated specimens were compressible and showed a slight decrease in compressive strength with 6% MNPs, although this value was higher compared to that of the scaffolds with no MNPs.