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Background/Objectives: Cardiac embryonic development is a highly coordinated and dynamic process governed by precise spatiotemporal gene regulation. Increasing evidence indicates that cellular heterogeneity and lineage specification during heart development are tightly controlled by complex gene regulatory networks (GRNs) and epigenetic mechanisms. Recent advances in single-cell multi-omics technologies provide unprecedented resolution to dissect these regulatory processes. This review aims to summarise current applications of single-cell multi-omics approaches to elucidate gene regulatory mechanisms underlying cardiac embryogenesis and their implications for congenital heart disease (CHD). Methods: We systematically reviewed recent literature on single-cell RNA sequencing (scRNA-seq), single-cell assay for transposase-accessible chromatin sequencing (scATAC-seq), spatial transcriptomics, and integrative multi-omics analyses applied to embryonic heart development. Studies were analysed to evaluate how these technologies contribute to cell-type identification, lineage trajectory reconstruction, GRN inference, and epigenetic landscape characterisation. Results: Single-cell multi-omics approaches have enabled the construction of high-resolution cardiac cell atlases, revealing previously unrecognised cellular heterogeneity and transitional states during heart development. Integrative analyses of transcriptomic and chromatin accessibility data have provided insights into lineage commitment, key transcription factors, enhancer-promoter interactions, and dynamic GRNs. These findings have advanced understanding of developmental genetics in cardiac morphogenesis and offered new perspectives on the molecular mechanisms underlying CHD. Conclusions: Single-cell multi-omics technologies provide a powerful framework for investigating gene regulatory mechanisms during cardiac embryogenesis. Continued methodological refinement and integrative analyses are expected to further clarify developmental processes and facilitate translational insights into CHD.