The invention relates to a pharmaceutical composition for treating Hashimoto's thyroiditis and a preparation method thereof. The pharmaceutical composition is composed of bupleurum, radix curcumae, prunella vulgaris, rhizoma Dioscoreae Nipponicae, thunberg fritillary bulb, radix scrophulariae, edible tulip, astragalus, dark plum and other components, and can be made into granules, capsules, tablets or pills by the conventional pharmaceutical processes. The pharmaceutical composition has the effects of soothing liver-qi stagnation, reducing phlegm, removing stasis, and softening hardness to dissipate stagnation, and applies to patients with Hashimoto's thyroiditis and thyroid nodules. Clinical studies have shown that the pharmaceutical composition can significantly improve the symptoms of Hashimoto's thyroiditis, reduce the thyroid volume and isthmus thickness, and reduce the level of TgAb and TPOAb, and the total effective rate is 97.22%. In addition, for patients with thyroid nodules, nodules can be significantly reduced or even disappeare, no significant adverse reactions are presented in the course of treatment. Experimental studies have shown that the pharmaceutical composition reduces the level of TgAb and TPOAb, and reduces inflammatory infiltration and thyroid follicular damage.