This invention discloses surface-silicon-coated near-infrared fluorescent magnetic nanocomposite particles, their preparation method, and applications, which belong to the intersection of nanotechnology and biomedicine. The invention involves embedding magnetic nanoparticles into silica particles in a microemulsion system together with near-infrared fluorescent quantum dots or near-infrared fluorescent organic dye molecules, forming surface-silicon-coated near-infrared fluorescent magnetic nanocomposite particles. These nanocomposite particles can also incorporate anticancer drugs as well as various biomolecules such as antibodies, ligands, peptides, cytokines, etc., that have targeting recognition functions. By utilizing the magnetic properties of the nanoparticles, quantum size effects, photothermal effects of light, and the pharmacological effects of anticancer drugs along with the recognition functions of biomolecules, the prepared nanocomposite particles are used for tumor treatment, offering broad application prospects in the medical field.