Advances in surgical and medical treatment for congenital heart disease have resulted in greater life expectancy. As a result, there has been an increase in the utilization of cross-sectional imaging for diagnosis and management of complex congenital heart disease. This manuscript describes a morphological and sequential segmental approach to deciphering the code of complex congenital heart defects in cross-sectional imaging, mostly computed tomography. This manuscript will review approaches to differentiate types of transposition, the anatomic relationships of cardiac structures, and the application of these relationships in the description of complex congenital heart disease.