Background: Geographic tongue and fissured tongue are both common oral mucous membrane diseases relatively. The treatment of this disease is typically causative therapy because of the unknown etiology, and other afflictions. Gastrointestinal disease is one of the factors that induce geographic tongue with a fissured tongue. As an adjuvant drug that can inhibit the growth of Helicobacter pylori, the most common pathogen of chronic gastritis, Lactobacillus is widely used in clinic. However, there are seldom studies about Lactobacillus used in the treatment of geographic tongue and fissured tongue. Therefore, this case we used typically causative therapy with Lactobacillus as adjuvant to treat patient with a geographic tongue and fissured tongue with gastrointestinal disease and explore the effectiveness for further application. Case Description: A 33-year-old female patient presented with a geographic tongue and fissured tongue with dysgeusia. At the first visit, there were smooth red lesions on the back of the tongue with the hyperplasia of the surrounding filiform papilla. The cracks in the middle of the tongue had a crack of about 2.5 cm long and 0.8 cm deep, and 5-6 light cracks on the tip of the tongue. The patient reported a history of chronic gastritis for 1 year, often with soft stool and gastroesophageal reflux disease. We administered drug treatment, including sodium bicarbonate tablets, Kangfuxin solution, compound chlorhexidine solution, and stomatitis spray. In addition, we suggested the patient use a yogurt machine to make and drink fresh yogurt with Lactobacillus as adjuvant everyday day and suggested a daily regimen of a light diet with no stimulating food, regular work, and sufficient rest. Ten days after the first visit, the symptoms were obviously alleviated. Twenty days after the initial diagnosis, the geographic tongue lesions had disappeared and the cracks had basically healed. The patient reported that the gastric symptoms had improved, and there was no soft stool or stomach discomfort. Conclusions: This study used Lactobacillus as the adjuvant with typically causative therapy in the treatment of geographic tongue and fissured tongue.