The invention discloses a lattice metal composite structure with a nanometer core-shell structure and a preparation method thereof. The method comprises the following steps: compounding an epoxy resin/acrylate compound emulsion with the nanometer core-shell structure by adopting a stepping emulsion process; uniformly coating the compound emulsion onto an inner surface of a lattice metal interlayer structure, thereby obtaining a light shock-insulating multifunctional structure material; and respectively coating a layer of epoxy resin/acrylate compound damping coating materials with the nanometer core-shell structure onto the surfaces of the upper and lower lattice metal panels and the lattice core. The method is used for realizing the preparation of the epoxy resin/acrylate compound damping coating-lattice metal composite material with the nanometer core-shell structure, not only can increase the damping coefficient of the material structure, can improve the vibration and noise reduction properties and can meet the multifunctional design requirements of light weight, vibration and noise reduction, but also has the advantages of convenience in construction, low cost and environmental protection. The method is suitable for application in engineering fields, such as transportation, buildings, space flight and aviation.