L-lysine (Lys) graft-functionalized boron nitride nanosheets (Lys@BNNS) were successfully prepared by a combination of mechanical sand-milling exfoliation and non-covalent bond modification. Lys@BNNS and hexagonal boron nitride (h-BN) were added to thermoplastic polyurethane (TPU) to prepare composites by liquid phase mixing and hot-pressing, respectively. The structure and morphology of Lys@BNNS were characterized by Fourier transform infrared spectrometer (FT-IR), thermal gravimetric analyzer (TGA), X-Ray diffraction (XRD), X-ray photoelectron spectroscopy (XPS), scanning electron microscope (SEM) and transmission electron microscope (TEM). The effects of different filler contents on the thermal conductivity and heat emission rate of the Lys@BNNS/TPU composites were explored. The results show that the thermal conductivity of the Lys@BNNS/TPU composite is increased by 160% compared with pure TPU, when the filler mass fraction reaches 5%. This is great significance for improving the reliability and service life of highly integrated electronic products.