Tissue engineering provides a potential way to develop degradable bone substitutes for bone defects. In biomedicine, magnetic nanoparticles hold immense potential in a vast variety of applications. Accordingly, the aim of this study was to develop magnetic nanofibrous scaffolds for bone tissue engineering by embedding iron-doped hydroxyapatite nanoparticles into a poly(lactic-co-glycolic) acid matrix. Transmission electron microscopy showed that iron-doped hydroxyapatite nanoparticles were needle-like crystals. X-ray diffraction demonstrated that the precipitates were HA crystals with low content of magnetite as a second phase. Synthetic nanofibrous scaffolds were porous network structures, as demonstrated by scanning electron microscopy (SEM). Moreover, the results of energy dispersive spectroscopy evidenced the calcium, phosphorous and iron elements distributed in the scaffold. The magnetization measurements confirmed that synthetic nanoparticles and PLGA/Fe-HA scaffold possessed typical characterization of superparamagnetic behaviour. Regarding the biological performance, rat bone mesenchymal stem cells were found to have a good adhesion and proliferation on the scaffolds via SEM and using a cell counting kit. Moreover, upon exposure to the static magnetic field, cells on the scaffold stepped over the fibres and grew inside the PLGA/Fe-HA scaffolds. The increased alkaline phosphatase activity and osteogenic factors expression demonstrated that osteoblastic differentiation in mesenchymal stem cells could be induced by the synergistic effect of a magnetic scaffold and a static magnetic field. In vivo study suggested that the PLGA/ Fe-HA scaffolds promoted the osteogenesis process with the synergistic effect of a static magnetic field. This scaffold has good biocompatibility and osteoinductive ability, therefore, it could be innovatively applied to bone regeneration as a potential scaffold.