The invention provides a rubber substrate wave-absorbing material and a preparation method thereof. The method comprises the following steps: adding an ethanol solution of a silane coupling agent to iron nanoparticles, and stirring; dropping acetic acid, adjusting the pH of the solution to 5, and performing ultrasound shaking and mechanical stirring in a water bath to obtain a mixed solution; centrifuging the mixed solution, and washing the mixed solution with water until an obtained solid has a pH of 7; drying the solid under vacuum to obtain surface modified iron nanoparticles; and filling the surface modified iron nanoparticles, a vulcanizing agent and rubber, kneading, and mixing uniformly, and thermally pressing to prepare a wave-absorbing patch. The wave absorbing material prepared by the method improves the filling amount of a wave absorbing agent in the rubber, maintains the good flexibility and mechanical properties of the rubber, increases the compatibility of the wave absorbing agent and the rubber, and a high-performance wave absorbing material is prepared. Few organic reagents are involved in the reaction process, and the method is conducive to environmental protection.