In this study, a series of magnetic polyurethane/Fe3O4 elastomer nanocomposites were prepared by covalently embedding novel thiacalix[4]arenes (TC4As) functionalized Fe3O4 nanoparticles (TC4As-Fe3O4) which contain macrocycles with reactive hydroxyl groups. Surface functionalization of Fe3O4 nanoparticles with TC4As macrocycles as unique reactive surface modifier not only gives specific characteristics to Fe3O4 nanoparticles but also improves the interphase interaction between nanoparticles and the polyurethane matrices through covalent attachment of polymer chains to nanoparticle surfaces. The novel synthesized TC4As-Fe3O4 nanoparticles were characterized by FTIR, XRD, TGA, VSM and SEM analysis. Furthermore, the effect of functionalization of Fe3O4 nanoparticles on the various properties of resulting nanocomposites was studied by XRD, TGA, DMTA, SEM, and a universal tensile tester. It was found that the functionalization of nanoparticles with TC4As affords better mechanical and thermal properties to polyurethane nanocomposites in comparison with unmodified nanoparticles. The SEM analysis showed finer dispersion of TC4As-Fe3O4 nanoparticles than unmodified Fe3O4 nanoparticles within the polyurethane matrices, which arising from formation of covalent bonding between TC4As functionalized Fe3O4 nanoparticles and polyurethane matrices. Moreover, the investigation of in vitro biocompatibility of novel nanocomposites showed that these samples are excellent candidate for biomedical use.