The invention provides a polymer-based heat-conducting composite material, and a preparation method and an application thereof. The composite material is prepared from, by volume, 5-30% of a metal-based heat-conducting and electric-conducting filler, 5-30% of a ceramic-based heat-conducting and insulating filler and 40-90% of a matrix. The composite material adopts a compound formed by compoundingcopper with the heat-conducting and insulating filler silicon carbide or boron nitride as a filler, so that the heat-conducting property of the polymer material is remarkably improved. The compositematerial has excellent comprehensive performances, utilizes the high heat conductivity of the metal material, also has high resistivity, and can be applied to heat diffusion in occasions with high requirements on the electrical insulation performance and other occasions needing heat diffusion management requirements, and has good market prospects in the fields of preparation of heat-conducting andheat-dissipating materials, microelectronics, electricians and electrics, light emitting diodes, heat exchange engineering, solar energy, lithium batteries, automobiles, aerospace and the like. The composite material a simple preparation process and excellent processability, and can be practically applied on a large scale.