Congenital heart diseases (CHD) are the most common birth defects, which severely effect humans healthy. The genetic factors in CHD have been increasingly became to be the focus of attention worldly. It is quite important to understand the critical role of genetic factors in the onset, development, and prognosis of CHD. Various genetic factors such as chromosomal numerical and structural aberrations, point mutations, gene splicing sites mutation, copy number variations, RNA mutations and epigenetics modifications, played important roles in the development of CHD. This article only focuses on the effeteness of chromosomal abnormalities, monogeneses, copy number variations, and de novo mutations with CHD.