Ischemia reperfusion injury(IRI) is a pathological process that occurs in numerous organs throughout the human body， which is a clinically significant disease with high morbidity and mortality, and involves complex developmental mechanisms. Mitochondrial damage is a key factor in IRI and plays a critical role in mediating the pathophysiological process of organs injury. Mitochondrial quality control (MQC) mechanisms are a series of adaptive responses that protect mitochondrial structure and function and ensure organs function after IRI. MQC includes mitochondrial fission, mitochondrial fusion, mitochondrial autophagy and mitochondria-dependent cell death, which interact with each other and are involved in the IRI process from multiple pathways. However, the mechanism of MQC's role in IRI has not been fully clarified yet. In this review, we present a summary of the regulatory mechanisms and pathological roles of MQC in IRI, provide new insights into future clinical treatment.