The invention belongs to the technical field of breeding of bamboo rats, and in particular discloses a medicine for preventing and treating stomatitis in bamboo rats and a preparation method of the medicine. The medicine for preventing and treating stomatitis in the bamboo rats is mainly prepared by the following materials through baking, extracting, mixing and drying: 9-12 parts of silicon dioxide, 5-8 parts of bentonite, 4-9 parts of quercetin, 3-8 parts of glutamine, 3-7 parts of ferrous sulfate, 2-5 parts of zinc sulfate, 2-5 parts of compound vitamins, 5-10 parts of radix glycyrrhizae, 5-10 parts of bur beggarticks herb, 3-8 parts of honeysuckle flowers, 2-8 parts of chamaesyce thymifolia millsp and 2-5 parts of fructus crataegi. The medicine for preventing and treating stomatitis inbamboo rats provided by the invention, in accordance with principles of cooperative matching and assistant matching, combines chemical medicines and natural Chinese herbal medicines; the medicine functions as absorbing saliva in mouths, promoting convergence of oral wounds, diminishing inflammation and inhibiting bacteria, and clearing heat and toxic materials; the medicine, based upon internal and external combination, can be used for effectively preventing and treating the stomatitis in bamboo rats and bring about benefits for healthy growth of the bamboo rats; in addition, the preparation method is simple; and various raw materials can be effectively combined.