The invention provides a pharmaceutical composition for treating hyperthyroidism. The pharmaceutical composition for treating the hyperthyroidism is prepared from, by weight, 10-20 parts of thunberg fritillary bulbs, 15-30 parts of calcined oyster shells, 15-30 parts of common selfheal fruit-spike, 10-20 parts of sparganii rhizoma, 10-20 parts of citron fruits, 10-20 parts of kelp, 6-15 parts of seaweed, 15-25 parts of salviae miltiorrhizae, 16-28 parts of rhizoma curcumae, 10-25 parts of radix polygoni multiflori, 10-20 parts of concha arcae, 5-15 parts of costustoot, 15-25 parts of rhizoma atractylodis macrocephalae, 20-30 parts of rhizoma alismatis and 15-25 parts of concha mauritiae. According to the pharmaceutical composition for treating the hyperthyroidism, the formula is scientific, the compatibility is proper, toxic and side effects do not exist in clinical application, the curative effect is obvious, and the relapse rate is low.