Background: Gestational diabetes mellitus (GDM) is associated with adverse myocardial remodeling and impaired cardiac function of fetus. Nevertheless, specific molecular mechanisms underlying type 1 GDM-induced fetal myocardial injury remain unknown. Therefore, this study proposes to identify possible molecular mechanisms using RNA-seq. Methods: A rat type 1 GDM model was developed using streptozotocin (STZ) (25 and 50 mg/kg), and weight and glucose tolerance of maternal and offspring were evaluated. Changes in markers of myocardial injury and oxidative stress identified by ELISA and biochemical kits in offspring hearts. Identification of differentially expressed mRNAs (DE-mRNAs) associated with myocardial injury in type 1 GDM offspring using RNA-seq. Proliferation, apoptosis, and oxidative stress were assessed in high glucose-induced H9C2 cells after exogenously modulating ATP Synthase Membrane Subunit E (ATP5me). Results: Maternal weight, glucose and glucose tolerance, and fetal weight and heart weight were reduced in the type 1 GDM model, especially in 50 mg/kg STZ-induced. Increased of creatine kinase-MB (CK-MB), cardiac troponin T (cTnT), hypersensitive C-reactive protein (hs-CRP), reactive oxygen species (ROS) and malondialdehyde (MDA) and decreased of superoxide dismutase (SOD) were observed in type 1 GDM offspring hearts. type 1 GDM offspring hearts exhibited disorganized cardiomyocytes with enlarged gaps, broken myocardial fibers, erythrocyte accumulation and inflammatory infiltration. RNA-seq identified 462 DE-mRNAs in type 1 GDM offspring hearts, which mainly regulate immunity, redox reactions, and cellular communication. Atp5me was under-expressed in type 1 GDM offspring hearts, and high glucose decreased Atp5me expression in H9C2 cells. Overexpressing Atp5me alleviated high glucose-induced decrease in proliferation, mitochondrial membrane potential, BCL2 and SOD, and increase in apoptosis, MDA, ROS, c-Caspase-3, and BAX in H9C2 cells. Conclusion: This study first demonstrated that ATP5me attenuated type 1 GDM-induced fetal myocardial injury. This provides a possible molecular mechanism for the treatment of type 1 GDM-induced fetal myocardial injury.