The invention discloses a pharmaceutical composition for treating hyperlipidemia and atherosclerosis. The pharmaceutical composition comprises: active components, the active components are puerarin, daidzin, genistin, soybean Aglycone, Actascoisoflavone Glucoside, Astragaloside II, Astragaloside IV, Formononetin, Mulberry A, Moranginin, Scopoletin, Sanggenone C, 1-deoxynojirimycin, Pueraria polysaccharide , a combination of two or more of Astragalus polysaccharide and Morus alba polysaccharide; and a pharmaceutically acceptable carrier. The pharmaceutical composition of the present invention can reduce the fat plaque area in the aorta of apoE- / -transgenic mice of atherosclerosis model, has the effect of regulating hyperlipidemia in mice, and can treat hyperlipidemia and atherosclerosis.