Peroxiredoxin Ⅲ (PrxⅢ) is a mitochondria-localized peroxidase that plays a key role in detoxifying hydrogen peroxide (HO) and preserving organelle homeostasis. While its antioxidant function is well established under physiological conditions, the role of PrxⅢ in the context of cardiac hypoxia/reoxygenation (H/R) injury remains incompletely understood. In this study, we investigated the protective function of PrxⅢ in cardiomyocytes exposed to H/R stress, a widely used in vitro model to mimic ischemia/reperfusion injury. Using H9c2 cells and primary neonatal rat cardiomyocytes, we found that PrxⅢ knockdown significantly increased mitochondrial HO accumulation, leading to excessive mitochondrial fragmentation, impaired mitophagy, and reduced cell survival following H/R. Western blot analysis revealed that mitophagy regulators Parkin and BNIP3 were upregulated under moderate oxidative stress but were markedly suppressed in PrxⅢ-deficient cells after H/R, indicating that mitophagy activation is sensitive to the degree of oxidative stress. These findings were confirmed in vivo using mt-Keima transgenic mice, which showed significantly reduced mitophagic flux in PrxⅢ knockout hearts subjected to ischemia/reperfusion. In addition, PrxⅢ loss impaired lysosomal acidification and proteolytic activity, further contributing to defective autophagic flux. Re-expression of PrxⅢ restored mitochondrial morphology, mitophagy activity, and lysosome function, highlighting its central role in maintaining mitochondrial quality control (MQC). Collectively, our results demonstrate that PrxⅢ mitigates mitochondrial oxidative damage and preserves MQC by coordinating mitochondrial dynamics, mitophagy, and lysosomal integrity. These findings suggest that PrxⅢ may serve as a promising therapeutic target for preventing cardiac injury induced by oxidative stress during ischemia/reperfusion.