Objective To analyze the effects of two imaging methods of CT angiography (CTA) and ultrasonic cardiogram (UCG) in the diagnosis of complex congenital heart disease (CCHD). Methods The imaging data of preoperative coronary CTA and UCG of 56 CCHD patients who were treated in our hospital in the past two years (February 2016 to February 2018) were collected. The surgical results were used as reference to compare the accuracy of the two imaging methods. Results Surgery found that there were 132 heart malformations (61 cases of intracardiac malformations and 71 cases of extracardiac malformations), and the total accuracies of preoperative coronary CTA and UCG were 93.94% and 87.12%, respectively (P>0.05). The accuracies of coronary CTA and UCG in the diagnosis of intracardiac malformation were 90.16% and 86.89% respectively (P>0.05). The accuracies of coronary CTA and UCG in the diagnosis of extracardiac malformation were 97.18% and 87.32% respectively, and the accuracy of coronary CTA was significantly higher than that of UCG (P<0.05). Coronary CTA and UCG images could show the location, shape, structure, morphology and other anatomical abnormalities of internal and external large blood vessels in the heart, and the coronary CTA images could show the large vascular malformations more clearly, and the UCG images could show the intracardiac malformations more clearly. Conclusion There is no significant difference in the total detection rate of CTA and UCG in CCHD disease. However, CTA is easier to observe the external structure of heart, and UCG can clearly show the internal malformations of heart, and the combined two has high diagnostic value.