The invention discloses a pharmaceutical composition for treating livestock and poultry dysentery and a preparation method thereof, belonging to the field of livestock and poultry pharmaceuticals technology. The pharmaceutical composition is prepared by extracting the active ingredients from crude drugs of radix sophorae flavescentis, Chinese mahonia, Chinese mosla herb, garlic, semen arecae and the like by adopting modes of acid water extraction, steam distillation and the like according to different properties of drugs, and is prepared into powder, granules and mixture. The pharmaceutical composition has the efficacies of clearing heat and eliminating dampness, and detoxifying and stopping dysentery, and is mainly used for treating dysentery infected by the livestock and poultry.