To investigate the application of H2 to alleviate cardiac ischaemia-reperfusion (I/R) injury in a PGC-1α-dependent manner. A rat in vitro myocardial I/R injury model was used, Western blot was used to detect the expression levels of apoptosis markers (Bax, cleaved caspase-3, Bcl2), inflammatory factors (IL-1β, TNF-α), mitochondrial fission (DRP1, MFF) and mitochondrial fusion (MFN1, MFN2, OPA1). HE staining was used to observe the effect of H2 on the myocardial tissue structure injured by I/R. Transmission electron microscopy (TEM) was used to observe the changes in the mitochondrial structure of myocardial tissue after I/R injury. Real-time quantitative PCR (qPCR) was used to detect the expression of PGC-1α in the myocardial tissue of rats after I/R injury and H2 treatment. H2 increases the expression level of PGC-1α, while the deletion of PGC-1α inhibited the therapeutic effect of H2. H2 can improve the changes of the myocardial tissue and mitochondrial structure caused by I/R injury. H2 treatment effectively inhibited the inflammatory response, and the loss of PGC-1α could inhibit the therapeutic effect of H2. The application of H2 can alleviate myocardial I/R injury, and the loss of PGC-1α weakens the protective effect of H2 on the I/R heart.© 2024 The Author(s). Journal of Cellular and Molecular Medicine published by Foundation for Cellular and Molecular Medicine and John Wiley & Sons Ltd.