Bio-compatible and superparamagnetic Fe3O4@Polydopamine nanocomposites with well-defined core/shell nanostructures have been successfully synthesized by using an in situ self-polymerization method. The size of the core/shell product can be controlled by varying the size of the central Fe3O4 core, and different thicknesses of the PDA shells are obtained by tuning the dopamine monomer concentration. The morphology, phase composition and crystallinity of the as-prepared nanocomposites have been characterized by transmission electron microscopy (TEM) and powder X-ray diffraction (XRD). The 5-dimethylthiazol-2-yl-2,5-diphenyl-tetrazolium bromide (MTT) cytotoxic analysis shows that the product is biocompatible, with a low toxicity. These unique core/shell materials would be applied in catalyst supports or drug delivery.Graphical abstractBio-compatible and superparamagnetic Fe3O4@Polydopamine nanocomposites with well-defined core/shell nanostructures have been successfully synthesized by using an in situ self-polymerization method. These unique core/shell materials could be applied in catalyst supports or drug delivery.Highlights► A facile in situ self-polymerization method was successfully developed to synthesize bio-compatible and superparamagnetic Fe3O4@Polydopamine (PDA) nanocomposites with well-defined core/shell nanostructures. ► The size of the core/shell product can be controlled by varying the size of the central Fe3O4 core, and different thicknesses of the PDA shells are obtained by tuning the dopamine monomer concentration. ► To the best of our knowledge, this is first report focused on the controllable synthesis of core/shell Fe3O4@PDA microspheres and the investigation of its cell viability. ► These unique core/shell materials would be applied in catalyst supports or drug delivery.