To observe the effect of Modified Xijiao Dihuang Decoction (, MXDD) on rats with radiation enteritis, and explore its action mechanism. Thirty female Sprague Dawley rats were divided into the control, model, dexamethasone (DXM), golden bifid (GB) and MXDD groups using random number table, 6 rats in each group. Except the control group, the other rats were developed into radiation enteritis model by exposing to a single 60Co-γ ray at a dose of 11 Gy. The rats in the DXM, GB and MXDD groups were treated with DXM (1.425 mg/kg), GB (0.8 g/kg) and MXDD (36.0 g/kg) for 3 days, respectively. Body weight and diarrhea condition of rats were evaluated daily. On day 3, the feces of rats were collected for intestinal flora detection and the small intestinal tissues were also collected. Bacterial species annotation, alpha and beta diversities as well as composition of intestinal flora were detected and compared. The protein and mRNA expressions of interleukin 17 (IL-17), retinoid-related orphan nuclear receptor gamma t (ROR-γt) and forkhead/ winged helix transcription factor p3 (FoxP3) were determined by Western blot and polymerase chain reaction, respectively. The abundance and diversity of intestinal flora as well as the proportion at the phylum and genus levels were assayed by 16S rRNA metagenome sequencing. Correlation between intestinal flora and Th17/Treg was analyzed by heatmap method. On day 1 to 3 after radiation, compared with the control group, the body weight in model group was decreased (P<0.05 or P<0.01). Compared with the model group, MXDD could alleviate weight loss and diarrhea caused by irradiation. At the phylum level, MXDD cause a significant increase in Firmicutes, and a decrease in Proteobacteria (P<0.05 or P<0.01). At the genus level, MXDD reduced the proportion of Escherichia Shigella (P<0.01). In addition, IL-17 and FoxP3 mRNA and protein expression levels were down-regulated and ROR-γt was up-regulated by MXDD treatment (P<0.05). Besides, Firmicutes and Lactobacillus were positively correlated with FoxP3 (r=0.73, 0.79, respectively; P<0.01), negatively correlated with IL-17 (r=0.66, 0.64, respectively; P<0.01 or P<0.05) and ROR-γt (r0.73, 0.81, respectively; P<0.01). Proteobacteria and Escherichia Shigella both had positive correlation with IL-17 (r 0.77, 0.57, respectively; P<0.01 or P<0.05 ) and ROR-γt (r=0.94, 0.79, respectively; P<0.01) and negative correlation with FoxP3 (r0.74, 0.65; P<0.01). MXDD could improve the survival status of irradiated rats by regulating the richness, diversity and composition of intestinal flora, and restoring the balance of Th17/Treg.