Hypoxia induces cardiomyocytes injury, which further triggers the occurrence and development of cardiovascular diseases. There is a paucity of specific treatment options available with proven efficacy. Chinese patented pharmaceutical product Salidroside (Sal) has potent efficacy on treating hypoxic injury. However, the molecular mechanism remains obscure. In the present study, a UPLC-QTOFMS-based metabolomic method combined with cell viability and apoptosis assays were established to explore the therapeutic mechanisms of Sal against hypoxic injury. Significant protective effects of Sal against inhibited cell viability and apoptosis induced by hypoxic injury were observed in the pharmacodynamic evaluation. Moreover, 40 significantly changed metabolites related to hypoxic injury were identified, of which, 26 can be significantly regulated by Sal. Metabolic pathway enrichment analysis revealed that the mechanisms of Sal against hypoxic injury may be attributed to modulating the disordered homeostasis of energy and lipid metabolism. The present study provides new experimental information on the pathogenesis of hypoxia, unravels the potential targeted metabolic pathways of Sal against hypoxia on the whole metabolic network and highlights the importance of metabolomics as a potential tool for deciphering drug-targeted metabolic pathways.