The invention relates to an MTM antifuse element structure and a preparation method thereof. The MTM antifuse element structure comprises a substrate and an insulation support layer arranged on the substrate; the insulation support layer is provided with a metallic interconnection layer, an antifuse bottom plate and an oxidation layer; the oxidation layer coats the metallic interconnection layer and the antifuse bottom plate; the antifuse bottom plate and the metallic interconnection layer are separated by the oxidation layer; the metallic interconnection layer is provided with connecting holes; the connecting holes extend to the metallic interconnection layer from the surface of the oxidation layer and are internally filled with metallic electrodes; the antifuse bottom plate is provided with antifuse holes which extend to the antifuse holes from the surface of the oxidation layer; the antifuse holes are internally filled with a high-resistance dielectric layer, an antifuse top plate and metallic electrodes in sequence; and the metallic electrodes are electrically connected with the antifuse top plate and the metallic interconnection layer. The technology in the invention has simple operation, high reliability, good compatibility and strong anti-radiation capability.