Objective To investigate the mechanism of AMP-activated protein kinase (AMPK) in hepatic ischemia-reperfusion injury (HIRI). Methods ① Grouping. Forty-two mice were randomly divided into Sham group, 4 ischemia reperfusion (IR) group of different times (2, 6, 12, and 24 h), Compound C group, and Compound C+repamycin (Rapa) group, each group enrolled in 6 mice. Compound C group: mice were modeled at 1 h after intraperitoneal injection of Compound C (25 mg/kg). Compound C+Rapa group: mice were modeled at 1 h after intraperitoneal injection of rapamycin (1 mg/kg) and Compound C (25 mg/kg). Mice of 4 IR groups, Compound C group, and Compound C+Rapa group were used to prepare HIRI model. Mice of Sham group were treated only for laparotomy, freeing the first portal hepatis and closing peritoneal. ② To filter the best IR time. The levels of alanine aminotransferase (ALT) and aspartate aminotransferase (AST) in the serum of mice in Sham group and IR groups of 4 different reperfusion time points were measured. The pathological changes of liver tissues were observed by HE staining, and the expressions of related proteins in liver tissue of mice were detected by Western blot. Considering the results of blood biochemical test, HE staining, and Western blot together to determine the best IR point. ③ The exploration of signal pathway for AMPK. The expressions of proliferating cell nuclear antigen (PCNA) were observed by immunohistochemical staining in the liver tissues of IR-12 h group, Compound C group (12 h after IR) and compound C+Rapa group (12 h after IR). The mitochondrial damage was observed by rhodamine 123 staining, and the apoptotic status of liver cells was detected by terminal deoxynucleotidyl transferase-mediated dUTP nick end labeling assay (TUNEL). Results ① The 12 h after IR was the best observation time point. Compared with IR-12 h group, the levels of ALT and AST in Sham group, IR-2, 6, and 24 h groups were lower (P<0.05). HE staining showed that liver tissue destruction in IR-12 h group was the most severe. Western blot showed that, expressions of AMPKα, phosphorylated adenylate activated protein kinase α (p-AMPKα), Nip3-like protein X (Nix), BCL-2 homologous water-soluble protein (Bax), as well as ratio of autophagy microtubule-associated protein light chain 3 (LC3)Ⅱto LC3Ⅰof Sham group, IR-2, 6, and 24 h group were all lower than those of IR-12 h group (P<0.05), but the expressions of phosphorylated mammalian target of Rapa (p-mTOR) of Sham group, IR-2, 6, and 24 h group were all higher (P<0.05). Therefore, 12 h after IR was the best time to observe. ② Compared with IR-12 h group, the expression level of PCNA protein in liver tissue of Compound C group was lower (P<0.05), the mitochondrial luminescence intensity was weaker and the apoptotic cells were more. Compared with Compound C group, the expression of PCNA protein in the liver tissue of the Compound C+Rapa group was higher (P<0.05), the mitochondrial intensity was stronger and the apoptotic cells were less. ③ Compared with IR-12 h group, the expressions of Nix and p-AMPKα, and ratio of LC3Ⅱ to LC3Ⅰ in liver tissue of Compound C group decreased (P<0.05), while the expressions of p-mTOR, Caspase-3, and Cleaved Caspase-3 increased (P<0.05). Compared with Compound C group, the expressions of p-AMPKα and Nix in the liver tissue of Compound C+Rapa group increased (P<0.05), while the expressions of p-mTOR, Caspase-3, and Cleaved Caspase-3 decreased (P<0.05). Conclusion During the HIRI in mouse, AMPK regulates mitophagy and apoptosis through the mTOR/Nix pathway.