Objective To observe the effects and to discuss the mechanism of dexmedetomidine on the intestinal fatty acid binding protein (I-FABP) and inflammatory factors of rats with intestinal ischemia-reperfusion injury. Methods The intestinal ischemia reperfusion injury model of rats was established and then rats were randomly divided into the sham operation group, ischemia-reperfusion group, and dexmedetomidine group. The aortic blood of rats was extracted at the 2 h and 6 h after ischemia-reperfusion. The plasma I-FABP levels were measured by ELISA. By the end of experiments, the contents of IL-6 and IL-10 in intestinal tissues were measured by ELISA. The intestinal tissues were stained by the HE and their injury severity was scored by the methods of Chiu's six levels. Results The plasma I-FABP levels of the ischemia-reperfusion group and dexmedetomidine group at 2 h and 6 h after reperfusion were significantly higher than those of the sham operation group. The differences were statistically significant (P<0.05). Compared to the ischemia-reperfusion group, the plasma I-FABP levels of the dexmedetomidine group were significantly decreased. The differences were statistically significant (P<0.05). The contents of IL-6 and IL-10 in intestinal tissues of the ischemia-reperfusion group and dexmedetomidine group were significantly higher than the sham operation group. The differences were statistically significant (P<0.05). Compared to the ischemia-reperfusion group, the contents of IL-6 in intestinal tissues of the dexmedetomidine group were lower, while the contents of IL-10 were higher. The differences were statistically significant (P<0.05). The Chiu's score of the dexmedetomidine group was significantly lower than that of the ischemia-reperfusion group but higher than that of the sham operation group. The differences were statistically significant (P<0.05). Conclusion Dexmedetomidine can effectively reduce the production of inflammatory factor after intestinal ischemia reperfusion, decrease the content of plasma I-FABP, and protect the intestinal functions.