The fabrication of a smart magnetically controllable bio-based polymeric nanocomposite (NC) has immense potential in the biomedical domain. In this context, magneto-thermoresponsive sunflower oil modified hyperbranched polyurethane (HBPU)/Fe3O4 NCs with different wt.% of magnetic nanoparticles (Fe3O4) were prepared by an in situ polymerization technique. Fourier-transform infrared, x-ray diffraction, vibrating sample magnetometer, scanning electron microscope, transmission electron microscope, thermal analysis and differential scanning calorimetric were used to analyze various physico-chemical structural attributes of the prepared NC. The results showed good interfacial interactions between HBPU and well-dispersed superparamagnetic Fe3O4, with an average diameter of 7.65 nm. The incorporation of Fe3O4 in HBPU significantly improved the thermo-mechanical properties along with the shape-memory behavior, antibacterial activity, biocompatibility as well as biodegradability in comparison to the pristine system. The cytocompatibility of the degraded products of the NC was also verified by in vitro hemolytic activity and MTT assay. In addition, the in vivo biocompatibility and non-immunological behavior, as tested in Wistar rats after subcutaneous implantation, show promising signs for the NC to be used as antibacterial biomaterial for biomedical device and implant applications.