The invention discloses a pharmaceutical composition for preventing and treating rheumatoid arthritis. The traditional Chinese medicine raw materials for constituting active ingredients of the pharmaceutical composition by weight are as follows: 5.5-6.0mg of berberine, 0.3-0.4mg of palmatine, 1.5-2.0mg of jatrorrhizine, 1.5-1.8mg of magnoflorine, 0.1-0.2mg of phellodendrine, 0.2-0.3mg of coptisine, 55-60mg of baicalin, 1.5-2.0mg of baicalein, 5.0-7.0mg of wogonoside, 0.03-0.05mg of wogonin, 20-25mg of geniposide, 0.1-0.2mg of crocin and 0.25-0.3mg of chlorogenic acid. The results of pharmacological tests show that the pharmaceutical composition can significantly reduce the disease severity of CIA mice with the rheumatoid arthritis, significantly improve the inflammation and the immune injury situation at lesion sites in comparison with a control group and be used for preparing drugs for preventing and treating the rheumatoid arthritis.