Impaired mitochondrial function is a key factor attributing to lung ischaemiaâreperfusion (IR) injury, which contributes to major postâtransplant complications. Thus, the current study was performed to investigate the role of mitochondrial autophagy in lung I/R injury and the involvement of the mTOR pathway. We established rat models of orthotopic left lung transplantation to investigate the role of mitochondrial autophagy in I/R injury following lung transplantation. Next, we treated the donor lungs with 3âMA and Rapamycin to evaluate mitochondrial autophagy, lung function and cell apoptosis with different time intervals of cold ischaemia preservation and reperfusion. In addition, mitochondrial autophagy, and cell proliferation and apoptosis of pulmonary microvascular endothelial cells (PMVECs) exposed to hypoxiaâreoxygenation (H/R) were monitored after 3âMA administration or Rapamycin treatment. The cell apoptosis could be inhibited by mitochondrial autophagy at the beginning of lung ischaemia, but was rendered out of control when mitochondrial autophagy reached normal levels. After I/R of donor lung, the mitochondrial autophagy was increased until 6Â hours after reperfusion and then gradually decreased. The elevation of mitochondrial autophagy was accompanied by promoted apoptosis, aggravated lung injury and deteriorated lung function. Moreover, the suppression of mitochondrial autophagy by 3âMA inhibited cell apoptosis of donor lung to alleviate I/Râinduced lung injury as well as inhibited H/Râinduced PMVEC apoptosis, and enhanced its proliferation. Finally, mTOR pathway participated in I/Râ and H/Râmediated mitochondrial autophagy in regulation of cell apoptosis. Inhibition of I/Râinduced mitochondrial autophagy alleviated lung injury via the mTOR pathway, suggesting a potential therapeutic strategy for lung I/R injury.