The invention provides a Mongolian medicine composition for treating thyroid diseases. The Mongolian medicine composition is prepared from deer horns, emblic leafflower fruits, Gentiana szechenyii, seabuckthom fruits, integripetal rhodiola herbs, medicine terminalia fruit pulp, common selfheal spike fruits, belleric terminalia fruits, corniculate spurgentian herbs, red bartsia, Chinese goldthreadrhizomes, sweet wormwood herbs, radix isatidis, madder herbs, loquat leaves, ural licorice roots, purple bergenia herbs and lobedleaf pharbitis seeds. The invention further provides a preparation method of a pill of the composition. The preparation method includes the steps: processing, sterilizing, mixing, crushing, stirring and screening raw materials to powdered medicines; gradually spraying purified water and adding powdered medicines to prepare large particles; gradually spraying purified water and adding powdered medicines after screening to prepare pills; screening and drying the pillsto obtain Mongolian medicine pills. The Mongolian medicine composition takes the deer horns, the lobedleaf pharbitis seeds and the common selfheal spike fruits as main raw materials, the medicine terminalia fruit pulp and the belleric terminalia fruits serve as three-root nursing medicines, the seabuckthom fruits serve as a stasis removing and blood diluting medicine, the emblic leafflower fruits,the red bartsia, the madder herbs and the corniculate spurgentian herbs serve as blood heat, badagan and xila removing medicines, the Gentiana szechenyii, the integripetal rhodiola herbs, the sweet wormwood herbs, the ural licorice roots, the loquat leaves, the radix isatidis and the purple bergenia herbs serve as heat clearing and toxicity removing medicines, the Chinese goldthread rhizomes serve as a pus and blood drying medicine. The Mongolian medicine composition is good in treatment effect.