To observe the clinical effect of Mongolian Medicine in treating pediatric indigestion, and provide theoretical proof for clinical treatment. Methods: One hundred and ten patients with pediatric indigestion admitted to our hospital from January 2010 to October 2012 were randomly divided into observation group and control group, with 55 patients in each group. In accordance with their ages and conditions, patients in the observation group were given oral administration of Mongolian medicine Tonglaga-5, 1 to 5 grams each time, 1 to 2 times a day; patients in the control group received oral administration of compound pancreatin powder (0.3 grams each package), 1 time a day. Both of the groups were given 2 treatment courses. Results: There were no significant differences on the score of appetite and symptoms between the two groups (P>0.05). After the treatment, the appetite score in observation group and control group were respectively 2.03±0.64 and 4.61±1.24, which showed significant differences (P<0.05). The total effective rate in observation group and control group were respectively 90.91% and 72.73%, which showed significant differences (χ²=4.950，P=0.026). Conclusion: The Mongolian medicine Tonglaga -5 used in treating pediatric indigestion regulates the whole body, showed no obvious adverse effects, significantly relieved the clinical symptoms of patients with satisfactory clinical effect.