The invention discloses a papaya Chinese herba preparation for treating chronic gastroenteritis and a preparation method thereof. The papaya Chinese herba preparation is prepared from the following raw materials in parts by weight: 200-220 parts of papaya, 40-60 parts of rhizoma coptidis, 50-70 parts of yam, 55-75 parts of hawthorns, 60-80 parts of wild chrysanthemum flowers, 55-75 parts of radix paeoniae alba, and 65-85 parts of honey. The preparation method comprises the following steps: firstly, cutting papaya, yam and hawthorns into slices, and drying and dehydrating the slices; then, mixing the obtained slices with rhizoma coptidis, wild chrysanthemum flowers and radix paeoniae alba, and decocting the obtained mixture, extracting by using 95% ethanol, after the obtained product is subjected to standing and liquid separation, concentrating the obtained product; and finally, adding honey, mixing, heating and modulating the obtained product, after the obtained product is cooled, sequentially carrying out fine filtration and ultraviolet disinfection, and carrying out vacuum metering and bottling on the obtained product, so that the papaya Chinese herba preparation for treating chronic gastroenteritis is obtained. A cydonic acid contained in the papaya adopted by the preparation disclosed by the invention has a strong anti-inflammatory and antibacterial effect, and has a significant inhibitory effect on various intestinal bacteria and staphylococcus; and supplemented by effective drugs for treating acute enteritis, the preparation can effectively treat diseases caused by acute enteritis.