Objective To investigate the effects of the physical parameters of radiotherapy and intestinal flora on the risk of secondary radiation enteritis (RE) in patients with abdominal malignant tumors. Methods Ninety-eight patients with malignant abdominal tumors who were treated with radiotherapy from April 2020 to August 2023 at Anyang District Hospital in Puyang City were selected and assigned to the RE group (n = 26) or the non-RE group (n = 72) . The clinical data, physical parameters of radiotherapy, and changes in the intestinal flora were compared between the two groups. Pearson’s correlation analysis was used to determine the correlation between the physical parameters of radiotherapy and changes in the intestinal flora, and logistic analysis was used to analyze the relationship between the physical parameters of radiotherapy, changes in the intestinal flora, and risk of RE. The receiver operating characteristic (ROC) curve and the area under the curve (AUC) were used to analyze the physical parameters of radiotherapy and changes in intestinal flora in predicting risk of RE. Results The doses of V20, V40, and D2cc in the small intestine, D2cc in the rectum, and D2cc in the colon were higher in the RE group than in the non-RE group (P < 0.05) . The α diversity Chao1 index, Shannon index, and Simpson index of the intestinal flora in the RE group were lower than in the non-RE group, at the third week of radiotherapy, and the decrease in the α diversity Chao1 index, Shannon index, and Simpson index of the intestinal flora in the RE group was greater than in the non-RE group, before and after radiotherapy (P < 0.05) . The doses of V20, V40, and D2cc in the small intestine, D2cc in the rectum, and D2cc in the colon were positively correlated with decreases in the α diversity Chao1 index, Shannon index, and Simpson index of the intestinal flora, before and after radiotherapy (P < 0.05) . The logistic analysis showed that the decrease in V20, V40, and D2cc in the small intestine, D2cc in the rectum, D2cc in the colon, α diversity Chao1 index, Shannon index, and Simpson index of the intestinal flora were independent risk factors for occurrence of RE (P < 0.05) . The AUC of the physical parameters of radiotherapy and changes in intestinal flora combined to predict the risk of RE as 0.920, which was greater than that of each indicator alone. Conclusion The physical parameters of radiotherapy are closely related to the changes of intestinal flora in patients with malignant abdominal tumors, which, in combination, can increase the risk of RE, and have a high predictive value for the risk of RE.