The invention discloses a pharmaceutical composition for treating climacteric syndrome and a preparation method thereof. The pharmaceutical composition is prepared from acanthopanax obouatus hoo, prepared rehmannia roots, cinnamon, prepared aconite, medlar, prepared ligustrum lucidum, yam, tuckahoe, prepared dodder, prepared cistanche salsa, tree peony barks and alisma orientale. The invention aims to solve the defects of the prior oral solid pharmaceutical composition for treating climacteric syndrome and provides a condensed pill which is smaller and is easy to swallow as well as is easily accepted by patients. The preparation method of the pharmaceutical composition for treating climacteric syndrome comprises the following steps: respectively crushing the yam, the cinnamon and the treepeony barks into fine powder, and mixing the fine powder for later use; adding ten times of water into other nine Chinese medicines comprising the prepared rehmannia roots and the like to carry out decoction twice, wherein the first decoction time is 2 hours, and the second decoction time is 1 hour; combining decoction liquors, and filtering; under the conditions of the temperature of 65-70 DEG Cand the pressure of -0.08MPa, depressurizing and condensing the filter liquor into clear paste with relative density of 1.08-1.12 at the temperature of 60-70 DEG C, cooling, adding the same amount ofalcohol, stirring, and standing for one night; filtering supernatant fluid, depressurizing and recovering alcohol, and condensing the supernatant fluid into clear paste with relative density of 1.20-1.25 at the temperature of 60-70 DEG C; mixing the clear paste and the fine power, depressurizing and drying, crashing the dry paste, screening by a sieve of 100 meshes, adding 10g of carboxyrnethyl starch sodium and a proper amount of starch, and mixing.