Cerebral ischemia/reperfusion injury (CI/RI) is a common clinical pathophysiological phenomenon after thrombus recanalization in stroke patients. Its pathogenetic mechanism involves multiple steps, of which mitochondria play a key role as "energy stations". Cerebral ischemic stroke induces remarkable changes in the expression of microRNAs (miRNAs) and long non‑coding RNAs (lncRNAs) in the brain, which indicates the association of miRNAs and lncRNAs of the complex pathological process after ischemic stroke. In addition, some related miRNAs and lncRNAs are found to participate in the development of CI/RI by regulating mitochondria. The current review is designed to summarize the effects of mitochondria on CI/RI, and the latest research findings about the involvement of miRNAs and lncRNAs to regulate CI/RI, so as to provide new targets and ideas for the prevention and treatment of CI/RI, as well as new thoughts and ideas for the prevention and treatment of CI/RI.