The invention discloses a preparation method of a graphene modified polyether-ether-ketone composite material. The preparation method comprises the following steps: step 1, weighing 100 parts by weight of polyether-ether-ketone, 1-5 parts by weight of carbon nanotubes, 1-5 parts by weight of carbon fibers, 5-10 parts by weight of graphene, 1-5 parts by weight of boron nitride and 0.5-3 parts by weight of a coupling agent; step 2, preparing graphene into graphene powder; 3, stirring and mixing polyether-ether-ketone, carbon fibers, the graphene powder, carbon nanotubes and thecoupling agent through a jet mill; and 4, feeding an obtained material from a main feed opening of a double-screw extruder, and mixing. According to the invention, the one-dimensional carbon nanotubes, the carbon fibers, the two-dimensional graphene and the boron nitride are added to form a three-dimensional network structure; the heat conduction performance, the frictional wear performance and the mechanical property of the polyether-ether-ketone composite material are improved, the jet mill is used for stirring and mixing, the crushing strength is high, and the combined operation of crushing, drying, crushing, mixing and the like can be realized in the machine; the energy utilization rate is high, energy is saved and loss is reduced.