We have explored the effect of boron in drinking water on the microstructure, mechanical barrier, immune barrier, antioxidant activity, and cell proliferation in rat jejunum. The treatment resulted in a significant increase in the jejunum villi height and ratio of villus height to crypt depth compared to the control group. The results showed that the jejunum villi height and ratio of villus height to crypt depth of the rats in experimental groups IV and V significantly increased compared with the control group (P < 0.05 or P < 0.01). Furthermore, boron treatment resulted in a significant increase in the number of rat jejunum goblet cells, intraepithelial lymphocyte and proliferating cell nuclear antigen positive cells as well as the concentration of secretory immunoglobulin A along with increased activity or content of total superoxide dismutase, glutathione peroxidase, and total antioxidant capacity. However, there was a decrease in expression of these markers in rats receiving the highest dosage of boron (640 mg/L). The results show that supplementing drinking water with low doses of boron could improve the microstructure of rat jejunum, enhance mucosal immunity, mechanical barrier function, and antioxidant activity, and promote cell proliferation.