The invention relates to a medicine composition for treating condyloma acuminate and a preparation method thereof. The medicine composition is prepared from the following raw materials: 50-100 parts of gentian, 50-100 parts of Spreading hedyotis herb, 50-100 parts of crape myrtle flowers, 40-80 parts of radix sophorae flavescentis, 40-80 parts of portulaca oleracea, 40-80 parts of densefruit pittany root-bark, 40-80 parts of radix isatidis, 40-80 parts of climbing groundsel herb, 40-80 parts of brucea javanica, 30-50 parts of radix angelicae dahuricae, 30-50 parts of amur cork tree bark, 20-40 parts of stellaria yunnanensis, 20-40 parts of angelica sinensis, 20-40 parts of fructus lycii, 20-40 parts of astragalus membranaceus, 20-40 parts of rhizoma atractylodis, and 15-30 parts of liquorice. The medicine composition with traditional Chinese herbs as raw materials further takes effect in treating condyloma acuminate through the roles in detoxifying to relieve internal heat, clearing away dampness-heat from lower jiao, benefiting qi and nourishing blood, and harmonizing yingfen and weifen; besides, the medicine composition is capable of regulating Qi, blood, Yin and Yang in viscera, improving the functional stage of human bodies for comprehensively improving physical fitness, and enhancing the immunologic function.