Objective: To investigate the efficacy of modified Gegen Qinlian decoction combined with probiotics in treating radiation enteritis (RE), and its regulatory effect on intestinal flora. Methods: A total of 40 patients with RE were enrolled. They were divided into an observation group (n=20) and a control group (n=20) according to the therapeutic regimen. The control group was treated with Clostridium butyricum capsules, while the observation group was treated with modified Gegen Qinlian Decoction in addition to the control group’s regimen. Both groups received 4 weeks of treatment. Changes in intestinal function indicators and intestinal flora before and after treatment were compared between the two groups, and clinical efficacy was evaluated. Results: After 4 weeks of treatment, the observation group showed a higher effective rate, higher fecal formation rate, and a lower defecation frequency compared to the control group (P<0.05). After treatment, the quantities of Bifidobacterium and Lactobacillus in the observation group were higher than those in the control group (P <0.05), while the quantities of Escherichia coli and Staphylococcus were lower than those in the control group (P <0.05). Conclusion: Combined use of modified Gegen Qinlian decoction and probiotics can improve clinical symptoms and restore the balance of intestinal flora in patients with RE, providing an effective regimen for clinical treatment.