Objective To study the effect of bone marrow mesenchymal stem cells transplantation on colon repair in rats with ulcerative colitis. Methods BMSCs male BALA/c rats were cultured in vitro. 75 male BALA/c rats were randomly divided into normal group, model group, low, medium and high concentration group with 15 rats each. UC rat model was induced by dextran sulfate sodium. 0.4ml saline was injected into tail vein of rats in normal group and model group. Rats in low, medium and high concentration groups were injected BMSCs suspension with tail vein 0.4ml, and the cell concentration was 0.5×106/ml, 1×106/ml and 2×106/ml respectively. The activity of rats and signs recorded by disease activity index (DAI) score, serum TNF-α, IL-6, IL-8, D-LAC and DAO content. A section of colon tissue in rats was sliced and observed under microscope. The other part was made into tissue homogenates to detect MPO content. Results After transplantation, the congestion and edema of the colon in the lower, middle and high concentration groups were better than that in the model group, and the ulcer and erosion decreased, and the inflammatory cells decreased. The levels of serum TNF-α, IL-6 and IL8 in the model group were significantly higher than that in the normal group (P＜0.05). The concentrations of TNF-α, IL-6 and IL-8 in the low, middle and high concentration groups were lower than those in the model group, and with the increase of the concentration, the levels of TNFα, IL-6 and IL8 in the groups decreased (P＜0.05). After transplantation, the content of serum D-LAC, DAO and tissue MPO in the model group and the low concentration group were higher than those in the other group after 7d (P＜0.05). The levels of serum D- LAC, DAO and tissue MPO in the rats of low, medium and high concentration groups after transplantation were not different from those in the normal group after 21d (P＞0.05). After transplantation seventh and 21d, the DAI scores of all groups decreased, and the low, middle and high concentration groups were lower than the model group, and with the increase of the concentration, the lower the DAI score (P＜0.05). Conclusion The transplantation of bone marrow mesenchymal stem cells (MSCs) in rats with ulcerative colitis can obviously improve the condition of rats, and may play an important role in inhibiting the inflammatory reaction and repairing the intestinal barrier. But the mechanism of the treatment still needs to be further studied.