Hepatic ischemia-reperfusion (I/R) injury, a common clinical complication of liver transplantation, gravely affects patient prognosis. Krüppel-like factors (KLFs) are a family of C2/H2 zinc finger DNA-binding proteins. KLF6, a member of the KLF family proteins, plays crucial roles in proliferation, metabolism, inflammation and injury responses; however, its role in HIR largely remains unclear. Herein, we found that KLF6 expression was significantly up-regulated in mice and hepatocytes after I/R injury. Subsequently, mice were subjected to I/R after tail vein injection of shKLF6- and KLF6-overexpressing adenovirus. KLF6 deficiency markedly aggravated liver damage and cell apoptosis along with the activation of hepatic inflammatory responses, whereas hepatic overexpression of KLF6 in mice showed opposite effects. Furthermore, we knocked out or overexpressed KLF6 in AML12 cells, and then exposed to hypoxia-reoxygenation challenge. KLF6 knockout significantly reduced cell viability, and increased hepatocyte inflammation, apoptosis, and ROS, whereas overexpression of KLF6 showed the opposite effects. Mechanistically, KLF6 inhibited the overactivation of autophagy at the initial stage, and the regulatory effect of KLF6 on I/R injury was autophagy-dependent. CHIP-qPCR and luciferase reporter gene assays confirmed that KLF6 was bound to the promoter region of Beclin1 and inhibited its transcription. Moreover, KLF6 activated the mTOR/ULK1 pathway. Finally, we retrospectively analyzed the clinical data of liver transplantation patients and observed significant associations between KLF6 expression and liver function after liver transplantation. In summary, KLF6 inhibited the overactivation of autophagy by transcriptional regulation of Beclin1 and activation of the mTOR/ULK1 pathway, thereby playing a protective role against hepatic I/R injury. KLF6 is expected to serve as a biomarker to predict the severity of I/R injury after liver transplantation.