Acute kidney injury (AKI) is one of a complex clinical syndrome with various causes and poor efficacy. The pathophysiology of AKI includes inflammation, cell apoptosis and cell death. Long noncoding RNAs (lncRNAs) represent a class of functional RNA molecules with a length of more than 200 nucleotide units (NT) and no ability to encode proteins. To identify novel molecular mechanism and potential targets for AKI, the differential expressed lncRNAs between normal and AKI tissues were analyzed with bioinformatics tool. In the present study, the mouse kidney ischemia/reperfusion injury (IRI) model and cell oxygen and glucose deprivation/ reperfusion (OGD/R) model were established. The expression levels of lncRNAs, miRNAs and mRNAs were detected by high-throughput sequencing technology. Meanwhile, lncRNA, miRNA expression levels were detected by quantitative real-time PCR. Luciferase analysis was used to further investigate the interaction between lncRNA AK154753 and miRNA, miRNA and mRNA. Western-blot were performed to test the expression of apoptosis related proteins. Furthermore, TUNEL assay was united with flow cytometry to detect cell apoptosis rate. We found lncRNA AK154753 was significantly up-regulated, while miR-345-3p and miR-708-5p were significantly down-regulated during IRI. At the same time, IRI triggered cell apoptosis both in vivo and in vitro as the evidence by upregulation of Bim/Bak/cleaved-caspase3. Luciferase analysis showed that lncRNA AK154753 could both interacted with miR-345-3p and miR-708-5p, miR-345-3p could interacted with Bak, miR-708-5p could interacted with Bim respectively. Inhibition of lncRNA AK154753 alleviated cell apoptosis along with miR-345-3p/miR-708-5p up-regulated during IRI. In conclusion, the results suggest that lncRNA AK154753 participates in the occurrence and development of acute kidney ischemia-reperfusion injury by regulating miR-345-3p/Bak, miR-708-5p/Bim axes. Inhibiting lncRNA AK154753 may represent new therapeutic modalities for renal IR injury.