To assess the therapeutic effects of probiotic oral therapy in pediatric patients with anorexia nervosa and to investigate its impact on intestinal flora composition, brain-gut peptide levels, and overall clinical outcomes. A retrospective study was conducted involving 100 children diagnosed with anorexia nervosa at Xingtang County People’s Hospital between January 2023 and June 2024. Patients were divided into two groups: a control group (n=50) receiving zinc gluconate oral solution alone and an observation group (n=50) receiving zinc gluconate plus probiotics. Outcome measures included intestinal flora analysis, brain-gut peptide levels (SS, NO), clinical efficacy, serum trace element levels (calcium, zinc, iron), and prognosis, including recurrence rates six months post-treatment. Baseline characteristics were similar between the two groups (P>0.05). After treatment, the observation group showed significantly higher levels of Bifidobacterium and Lactobacillus and lower levels of Enterobacter compared to the control group (P<0.05). Additionally, the observation group had lower levels of SS and NO (P<0.05), indicating improved brain-gut communication. Clinical efficacy was significantly higher in the observation group (P<0.05), with improved serum trace element levels (P<0.05 for calcium, zinc, and iron). Furthermore, the recurrence rate six months post-treatment was significantly lower in the observation group compared to the control group (P<0.05). Probiotic supplementation in children with anorexia nervosa effectively modulates intestinal flora, improves brain-gut peptide levels, and enhances clinical outcomes.