The invention discloses a pharmaceutical composition, and a preparation method, preparation and application thereof. The pharmaceutical composition is prepared from the following raw materials in parts by weight: 200-400 parts of Yushu, 800-1200 parts of Tinospora crispa, 800-1200 parts of belamcanda rhizome, 500-1500 parts of ginger, 500-2500 parts of motherwort, 100-300 parts of pepper and 200-400 parts of dried ginger. The preparation method comprises the following steps: respectively extracting, concentrating and drying to obtain the pharmaceutical composition. Pharmaceutically acceptable adjuvants can be added into the pharmaceutical composition to prepare powder, tablets, capsules, granules, dripping pills or honeyed pills. The invention also discloses application of the pharmaceutical composition in preparation of medicines for treating irregular menstruation. The Yushu used as the main medicine has the effects of tonifying fire to strengthen the body, eliminating wind, promoting blood circulation, alleviating pain, promoting the subsidence of swelling and dissipating blood stasis; the dried ginger and pepper used as adjuvants can assist the main medicine to enhance the curative effect; the ginger has the effects of invigorating yang and restoring menstrual flow; the motherwort has the effects of activating blood circulation to dissipate blood stasis, and inducing menstruation to relieve menalgia; and the Tinospora crispa and belamcanda rhizome have the effects of replenishing water, moistening, replenishing essence and tonifying the marrow. By combining all the components in the formula and matching cold and heat, the pharmaceutical composition can treat irregular menstruation.