The invention discloses a thermoplastic polymer matrix heat conduction composite material, and a preparation method and an application thereof. The heat conduction composite material contains a matrix and a filler filled in the matrix, the matrix is a thermoplastic polymer, the filler is modified hollow glass microspheres, and the modified hollow glass microspheres are hollow glass microspheres with the surface coated with heat conduction powder, obtained after the modification treatment of the surface by the heat conduction powder. The adoption of a thermoplastic plastic as the matrix realizes the good dispersion of the heat conduction powder and guarantees the processing performances of the material; and the adoption of the reasonable matching of the modified hollow glass microspheres and the heat conduction powder makes the material have the advantages of light weight, corrosion resistance, high heat conduction efficiency, good mechanical properties, easy machine shaping, no pollution, low cost, high precision, long life, good electric insulation and the like, so the material can be used in electronic and electric appliance product radiating fins, LED light fixture heat radiation pedestals, bearing heat radiation layers, and other fields having high heat conduction requirements.