Congenital heart diseases (CHD) are the leading cause of mortality associated with birth defects. Significant advancements have been made in comprehending the genetics of CHD through Whole Genome Sequencing (WGS) and Whole Exome Sequencing (WES) technologies. Cell and animal models have emerged as reliable choices to gain insights into the specific genetic mechanisms and factors underlying CHD. Human induced pluripotent stem cells (iPSCs) offer a novel approach for studying CHD by generating patient-specific iPSC-derived cardiomyocytes for related research. The utilization of CRISPR-Cas9 gene editing tools enables the introduction or correction of variant genes in iPSCs, facilitating a more comprehensive exploration of variant pathogenicity and molecular basis in CHD. In this review, we discuss the genetic progress achieved through genome sequencing in relation to CHD while also exploring how gene editing techniques and patient iPSCs contribute to our understanding of the genetic mechanisms underlying CHD. We highlight the significance of combining these two approaches for disease research, providing valuable insights for clinical investigations on the mechanism behind CHD.