Hypobaric hypoxia (HH) is the primary challenge at high altitude. Prolonged HH exposure impairs right cardiac function. Mitochondria-associated membrane (MAM) plays a principal role in regulating mitochondrial function under hypoxic conditions, but the mechanism remains poorly understood. In this study, proteomics analysis identified that PACS2, a key protein in MAM, and mitophagy were down-regulated in HH conditions. Metabolomics analysis indicated suppression of aerobic oxidation of glucose and fatty acids. Cardiomyocyte Pacs2 deficiency disrupted MAM formation and endoplasmic reticulum (ER)-mitochondria calcium flux further inhibiting mitophagy and mitochondrial energy metabolism during HH exposure. Overexpression of Pacs2 reversed these effects. Cardiac-specific knockout of Pacs2 exacerbated mitophagy inhibition, cardiomyocyte injury and right cardiac dysfunction induced by HH. Knock-in of Pacs2 recovered HH-induced RV structural and functional impairment. Thus, PACS2 is essential for protecting cardiomyocytes through mechanisms of ER-mitochondria calcium flux, mitophagy, and mitochondrial energy metabolism, thereby maintaining right cardiac function at high altitude.