To investigate the role of miR-146a / Sirt6 signaling-mediated autophagy in dexmedetomidine (DEX) treatment of intestinal ischemia-reperfusion ( I/ R) injury. Methods SD rats were randomly assigned to Sham, I/ R, and DEX groups with eight rats in each group. Except for the Sham group, the other groups underwent intestinal I/ R modeling. Rats in the DEX group were treated by an intraperitoneal injection of 25 μg / kg DEX at 30 min before ischemia. In vivo, intestinal histopathological examination and scoring were performed. In vitro experiments, the rat small intestinal crypt epithelial cell line IEC-6 was treated with DEX before deprivation / reoxygenation (OGD/ R) treatment. IEC-6 cell viability was analyzed by MTT assays. Apoptosis and miR-146a expression in intestines and IEC-6 cells were detected by TUNEL and quantitative real-time PCR, respectively. Sirt6 and LC3 expression in intestines and IEC-6 cells was detected by Western blot and immunofluorescence. Results Histopathological analysis indicated that DEX treatment protected against I/ R-induced intestinal epithelial damage and restored cell proliferation after OGD/ R exposure in a dose-dependent manner. Compared with the I/ R group, apoptosis in intestinal tissue of the DEX group was decreased significantly (P<0. 01), and of miR-146a, Sirt6 and LC3Ⅱ expression was increased significantly (P<0. 05). Consistent with the in vivo result, DEX significantly attenuated OGD/ R-induced apoptosis of IEC-6 cells (P<0. 01) and significantly increased the expression of miR-146a, Sirt6 and LC3Ⅱ in IEC-6 cells in vitro ( P < 0. 01). Furthermore, miR-146a inhibitor treatment of IEC-6 cells supported that miR-146a inhibition attenuated DEX-induced improvement and inhibited autophagy activation by downregulating Sirt6 expression. Conclusions DEX has a protective effect against I/ R injury by regulating miR-146a / Sirt6-mediated autophagy.