The present invention discloses a magnetic nanodrug for treating thrombosis, which comprises a core formed of magnetic nanoparticles, a shell enveloping the core and made of carboxyl-functionalized polyaniline, and a thrombosis-treatment drug covalently bonded to the shell. The magnetic nanodrug of the present invention is non-toxic to vascular endothelial cells, has superior stability, features superparamagnetism, and can be uniformly dissolved in water. Therefore, the magnetic nanodrug for treating thrombosis can be guided by an external magnetic field to concentrate on a specified region and increase the effect of thrombosis treatment.