The invention discloses a method for preparing a nanometer system for multi-model diagnosis and treatment integration. The method comprises the following steps: adopting an in-situ growth nanogold modified rare-earth upconversion nanoparticle method to perform ligand exchange modification on oil-soluble upconversion luminescence nanoparticles of citric acid with a core-shell structure to be water-soluble, and performing citric acid ligand modification on the surfaces of the nanoparticles; uniformly growing nanogold particles on the surface through an in-situ crystal growth method so as to obtain in-situ growth nanogold modified upconversion luminescence nanoparticles; and linking polyethylene glycol-adriamycin hydrochloride containing hydrazone bonds and thiol onto the nanogold surface, thereby obtaining the rare-earth upconversion nanometer system. The invention further provides the nanometer system and application thereof. The nanometer system provided by the invention is uniform in size, high in stability and high in biocompatibility, has the effects of chemotherapy and photo-thermal physiotherapy and can be applied to the fields of upconversion fluorescence imaging, magnetic resonance imaging, anti-cancer drug delivery, photo-thermal physiotherapy of cancers and the like.