The invention provides a pharmaceutical composition for treating spleen deficiency and a preparation method thereof. Based on parts by weight, the preparation method of the pharmaceutical composition comprises the following steps of: mixing 3-5 parts of ginseng, 3-5 parts of dangshen, 5-10 parts of astragalus membranaceus and 15-25 parts of angelica, and adding ethanol for extracting; mixing 15-25 parts of radix paeoniae alba, 8-13 parts of pericarpium citri reticulatae, 8-13 parts of elecampane, 8-13 parts of yam, 8-13 parts of hyacinth bean, 8-13 parts of licorice, 15-25 parts of ligusticum wallichii, 5-10 parts of cinnamon, 1-3 parts of rattletop, 1-3 parts of radix bupleuri, 1-3 parts of fructus alpiniae oxyphyllae, 1-3 parts of Sichuan pepper,1-3 parts of monkshood, 1-3 parts of rhizoma zingiberis and 10-15 parts of dogwood, and adding pure water for extracting; mixing 15-25 parts of poria cocos, 15-25 parts of bighead atractylodes rhizome and 5-10 parts of cassia twig, adding cellulose, extracting through water, inactivating the extracting solution for later use, mixing the extracting solutions, carrying out vacuum freeze drying to obtain solid dry paste of a drug extract, and carrying out superfine grinding and pelletizing to prepare the necessary pharmaceutical composition. The pharmaceutical composition provided by the invention is scientific in formula, suitable for mass production, free of untoward effect, strong in potency, quick to become effective and convenient to take.