Abstract: Objective To explore the effect of transplantation method with side population cells from intestinal mucosa on short bowel syndrome in rats. Methods The side population cells were isolated from the intestinal mucosa of infant Wistar rats(donors) at gestational age of 4 weeks and transplanted into 20 female rats(receptor) to establish the short bowel syndrome model.The effect of cell transplantation,basic Characteristics and absorption to nutritional substances of small intestine were compared between the two groups. Results The weight after the treatment of the rats in both groups showed a trend of increasing,and increase in the experimental group was significantly higher than that in the control group,and the difference was significant(P＜0.05);the humidity,length and area of small intestine in the experimental group were higher than that of the control group,the difference was significant(P＜0.05);the absorptivity of xylose and fat,and nitrogen-use efficiency in the in the experimental group were higher than that of the control group,the difference was significant(P＜0.05);the intestinal villus height and depth of the crypts in the experimental group were lower than that of the control group,but the density was higher than that in the control group,the difference was significant(P＜0.05). Conclusion The transplantation method with side population cells from intestinal mucosa can effectively improve the ability of small intestine to absorb nutrition in rats with short bowel syndrome,and has certain guiding significance in clinical application.