The invention discloses a pharmaceutical composition for treating gastroenteritis and a preparation method, a preparation and an application thereof. The pharmaceutical composition comprises the following raw materials in parts by weight: 20-150 parts of Costustoot, 20-100 parts of wrinkled giant hyssop, and 10-80 parts of Corydalis saxicola. The pharmaceutical composition is obtained by pre-treatment, extraction and post-treatment. The tablets, powder, capsules, a particulate agent and pill prepared by the pharmaceutically acceptable auxiliary materials can be added in the pharmaceutical composition for treating gastroenteritis, which is the application of the pharmaceutical composition for treating gastroenteritis. The raw materials are combined for synergism, and have the functions for clearing heat and removing dampness as well as rectifying qi and relieving pain, and the pharmaceutical composition is used for treating gastroenteritis.