Objective To investigate the curative effect and possible mechanism of berberine in treatment of rats with acute radiation enteritis. Methods Thirty-two male SD rats were randomly divided into blank control group, model group, berberine group and dexamethasone group (8 rats each). Rats in blank control group received pseudo-irradiation, and in remaining groups were irradiated with 12 Gy ⁶⁰Co γ ray to establish acute radiation enteritis model. Rats in berberine group were given 50 mg/(kg.d)berberine by gavage, in dexamethasone group were given 0.12 mg/(kg.d) dexamethasone by gavage, and rats in model group and blank control group received gavage with the same amount of normal saline. All the gavage continued for 7 days, then the serum and intestinal tissue of rats were taken and stored for later use. The weight and defecation of rats were observed, HE staining was performed to observe the histopathological changes of rat intestinal tissues and count the number of crypts, Masson staining was used to observe the deposition of collagen fibers in rat intestinal tissues, and ELISA was performed to detect the levels of interleukin-6 (IL-6), tumor necrosis factor-α (TNF-α), IL-1β and lipopolysaccharide (LPS). The content of malondialdehyde (MDA) and the activity of superoxide dismutase (SOD) in intestinal tissues were detected with test kit. The IEC-6 cells were divided into blank control group,model group, berberine group and dexamethasone group. IEC-6 cells in blank control group received pseudo-irradiation, in the rest groups were used to establish the IEC-6 cell radiation damage model, and each group was added with the corresponding medicine serum and co-cultured. qPCR was performed to detect the expression levels of IEC-6 cytochrome C, Bax, Bcl-2, and caspase-3 mRNA in each group. Results The body weight and defecation of rats in berberine group were better than those in dexamethasone group (P<0.05); no obvious intestinal structure damage was found and the proliferation of collagen fibers reduced significantly in rats of berberine group. The number of intestinal crypts was significantly more in berberine group than in model group (173.67±2.33 vs. 115.67±1.45, P<0.05), while no significant difference on the number of intestinal crypts existed between berberine group and dexamethasone group (P>0.05). The levels of IL-6, TNF-α, IL-1β, and LPS in the intestinal tissues of rats were significantly lower in berberine group than in model group, and the IL-6 level was lower in berberine group than in dexamethasone group (P<0.05). The MDA content was significantly lower and the SOD activity was increased in both berberine group and dexamethasone group than in model group (P<0.05), and the MDA content was lower in berberine group than in dexamethasone group (P<0.05). Compared with model group, the expression levels of Bax, caspase-3 and cytochrome C mRNA in IEC-6 cells decreased significantly in berberine group and dexamethasone group, and of Bcl-2 mRNA increased significantly (P<0.05). But no significant difference existed in the expression levels of Bcl-2, Bax, caspase-3 and cytochrome C mRNA in IEC-6 cells between berberine group and dexamethasone group (P>0.05). Conclusion Berberine can effectively improve the inflammatory response of acute radiation enteritis and protect intestinal crypts, the mechanism may be related to reducing the oxidative stress of intestinal tissues and regulating the expression of apoptosis protein in IEC-6 cells.