Tyrosine kinase inhibitors (TKIs) have been widely used for cancer chemotherapy, but they also cause cardiotoxicities in cancer patients. In this study, we used human stem cells as an in-vitro system to interrogate the mechanisms underlying drug-induced toxicity in differentiated cardiomyocytes, including anticancer tyrosine kinase inhibitor (TKI) drugs, including imatinib, sunitinib, and vandetanib. Sublethal TKI exposure produces multiple effects, including disarranged sarcomere structure, interrupted Ca2+-handling, and impaired mitochondrial function, evident of TKI-induced toxicity in differentiated cardiomyocytes. GATA4-mediated regulatory networks, including key mitochondrial target genes, emerge as significant molecular signatures in integrated analyses of transcriptome and chromatin accessibility dynamics. We find that, on a molecular level, GATA4 acts as a regulatory factor in mitochondrial biogenesis and OXPHOS by directly regulating specific metabolism-related genes, such as PPARGC1A. Functional genomic experiments targeting GATA4 reveals that GATA4 upregulation by CRISPR-activation is able to restore mitochondrial morphology and OXPHOS upon TKI exposure. In addition, we also identified that GATA4 is involved in regulation of mitochondrial biogenesis during early cardiac differentiation; inhibition of GATA4 during differentiation reduces mitochondrial DNA content, ATP production, and OXPHOS in differentiated cardiomyocytes, demonstrating a developmental role of GATA4 in metabolic management during early cardiac differentiation. Altogether, our study identifies a novel link between GATA4 and mitochondria in cardiomyocytes, and identifies GATA4 as a promising therapeutic target for reducing TKI-induced cardiotoxicity for human health.