Polyaryl-ether-ether-ketone (PEEK), an alternative to metal alloys in prosthesis implants, suffers from insufficient elasticity and biocompatibility, and generates wear particulates initiating the destructive osteolysis process. In this study coating the implant with Nb containing graphite-like carbon (GLC) film is performed using the closed field unbalanced magnetron sputtering system, the as-deposited Nb/GLC film is uniform and smooth. The mechanical assessment shows that Nb/GLC film has the strongly adhesive strength and good matching compliance to the flexible PEEK substrates. Especially, the use of GLC film not only effectively reduced the wear-generated debris in simulated body fluids but also exhibited excellently low friction character, as well as the lowest wear of the counterpart. Furthermore, Nb/GLC matrix greatly improved the biocompatibility and osteogenesis of PEEK by the indication of the excellent adherent attachment, proliferation and differentiation of L-929 fibroblast-like cell.