The invention relates to a preparation method of an array carbon nanotube/carbon fiber/silicon carbide thermally conductive composite material. According to the invention, the array carbon nanotube/carbon fiber/silicon carbide thermally conductive composite material is obtained through the steps of degumming, array carbon nanotube growth, polycarbosilane impregnation, PCS pyrolysis and repeated cyclic impregnation and pyrolysis. The obtained composite material has good mechanical performance, excellent high-temperature resistance, oxidation resistance, high thermal conductivity and the like. The material has bending strength higher than 125MPa, compressive strength higher than 500MPa, and thermal conductivity higher than 10W/(m.K). The material can endure 800-1200 DEG C high-temperature ablation in air for a long time. The method is simple, and has the advantages of low cost and low energy consumption. The method does not need high-temperature hot pressing, and has low requirement on equipment.