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Background: As a common and frequent disease in pediatric patients, pediatric anorexia (PN) poses a serious threat to childhood growth and health. In recent years, societal changes in lifestyle and diet have increased the incidence of this PN, which has attracted extensive attention from both the medical community and parents. It has been shown that massage therapy represents an effective intervention for the treatment of anorexia, but investigation on its mechanism(s) of action remains limited. In this study, we will explore the biological mechanism(s) of PN from the perspective of intestinal flora, to further reveal its site of action and therapeutic mechanism(s). Methods: A total of 60 healthy children will be randomly selected for physical examination. According to a random number generated by a computer, children with anorexia who meet the inclusion criteria will be selected. In strict accordance with the time sequence of inclusion, subjects will be randomly assigned to either the massage or control group (n = 60 per group). The blank group will receive no treatment. Children in the massage group will receive a designated massage protocol. The control group will be administered oral Jianweixiaoshi tablets over 4 weeks. Each group will be compared for intestinal flora structure, fecal short chain fatty acids levels, serum trace elements, urine D-xylose-excretion rates, gastric fluid emptying, gastric motility, and hemoglobin levels before and after treatment. Results: We will review the clinical trial registry in China (http://www.chictr.org.cn/searchprojen.aspx), peer-reviewed journals and academic conferences. Conclusion: This study will verify the intervention mechanism(s) of pediatric massage on intestinal flora and host metabolism in children with anorexia. Trial registration number: ChiCTR2000033274