The invention discloses an inorganic-inorganic nano hybrid material of a bimodal mesoporous core-shell structure as well as a preparation method and an application of the inorganic-inorganic nano hybrid material. The bimodal mesoporous inorganic-inorganic nano hybrid material of the core-shell structure is prepared by the following steps: firstly, with the presence of a surfactant, reducing metal salt by virtue of ascorbic acid, so that mesoporous inorganic nanoparticles are obtained; then, covering the surface of hexadecyl trimethyl ammonium bromide, which serves as a surfactant, with a layer of mesoporous silicon dioxide; covalently grafting diethyltriamine pentaacetic acid after modifying a mesoporous silicon dioxide shell layer by virtue of amino; and finally, coordinating with metal ions, so that the bimodal mesoporous inorganic-inorganic nano hybrid material of the core-shell structure is obtained. The prepared material has the core-shell material, wherein a core is constituted by the mesoporous inorganic nanoparticles and a shell is formed by the mesoporous silicon dioxide shell layer, and the surface of the mesoporous silicon dioxide shell layer is hybridized and modified by virtue of inorganic metals. The inorganic-inorganic nano hybrid material has the advantages of being uniform in dimension, good in biocompatibility and the like, and the inorganic-inorganic nano hybrid material is high in optical stability, high in photo-thermal conversion rate and high in magnetic resonance imaging resolution ratio; and integration of magnetic resonance imaging and photo-thermal therapy can be achieved.