The invention relates to a preparation method of a difunctional mesoporous silicon ball composite targeted drug delivery system, and belongs to the field of nanobiomedicine. The method comprises the steps that a coprecipitation method is adopted for preparing superpara magnetism Fe3O4 nanoparticles, then, hexadecyl trimethyl ammonium bromide is used as a template, a photosensitizer is doped, accordingly, the surfaces of the magnetic nanoparticles and the photosensitizer are wrapped by a layer of mesoporous silica, covalent linkage and physical absorption of anti-cancer medicine are achieved, finally, surface modification is carried out through folic acid and hyaluronic acid, and the difunctional mesoporous silicon ball composite targeted drug delivery system is obtained. According to the system, multiple effects of nuclear magnetism radiography, fluorescence imaging, magnetic hyperthermia, photoactive therapy and chemotherapy are integrated, diagnosis and treatment are integrated, magnetic targeting and FA/HA dual receptor-mediated targeting effect can more effectively enhance the targeting combination of the medicine and tumor cells, the effective concentration of the medicine in the tumor parts is improved, effect enhancement and toxicity reduction are achieved, the killability for the cancer cells is enhanced through dual drug loading, and the treatment effect on tumors is remarkably improved. The product obtained through the preparation method has a quite large application prospect in the field of medicine control release.