Mitochondrial dysfunction during lung ischemia-reperfusion injury (LIRI) contributes to organ dysfunction. Aconitase-2 (ACO2), by enhancing the mitochondrial tricarboxylic acid (TCA) cycle in pulmonary vascular endothelial cells (PVECs), plays a critical role in maintaining cellular energy metabolic homeostasis. Single-cell RNA sequencing was performed to characterize cellular phenotypes within the lung tissue microenvironment of I/R mice, and bulk RNA sequencing was applied to identify differentially expressed genes associated with LIRI. Our clinical cohort included 65 healthy donors and 48 patients with LIRI to evaluate the correlation between serum ACO2 levels and lung function. In vivo, using a murine I/R model, we administered an adeno-associated virus for lung-specific ACO2 overexpression, as well as an ACO2 inhibitor (tricarballylic acid), to assess their effects on lung injury. In vitro, primary PVECs were isolated and subjected to hypoxia/reoxygenation (H/R), followed by ACO2 overexpression or knockout, and treatment with the ACO2 downstream metabolite derivative 4-octyl itaconate (4-OI), to investigate its role in mitochondrial function and apoptosis. Serum ACO2 levels were reduced in LIRI patients and exhibited a significant negative correlation with impaired lung function. In I/R mice, ACO2 overexpression ameliorated mitochondrial dysfunction and attenuated lung injury, whereas ACO2 inhibition exacerbated these pathological changes. In PVECs, ACO2 overexpression enhanced mitochondrial function and reduced apoptosis; conversely, ACO2 knockout exerted opposing effects. Notably, supplementation with 4-OI mitigated mitochondrial dysfunction and cellular apoptosis induced by ACO2 deficiency. These findings suggest that ACO2 has therapeutic potential in improving mitochondrial function, reducing apoptosis, and alleviating LIRI, positioning it as a promising target for the treatment of this condition.