Objective To explore the clinical value of ultrasound combined with 64- slice CT in the diagnosis of complex congenital heart disease to improve the accuracy of diagnosis. Methods 62 patients who had complex heart disease and were admitted into the hospital during March 2013 to March 2015 were selected as the research objects. All patients received ultrasound and 64-slice CT examination before surgery. Based on the results confirmed by surgery, the diagnostic accuracy of ultrasound, 64-slice CT and the combination of the two was compared. Results Confirmed by surgery, there were a total of 158 cardiac malformations in the 62 cases of patients. Sequential segmental analysis showed that there were 82 malformations in the junction of intra-heart and atrioventricular, 48 malformations in the junction of cardiac large vessels and 28 malformations in extracardiac large vessels. The diagnostic accuracy rate of ultrasound was 91.8% (145/158) while of CT was 91.1% (144/158) and of combined detection was 97.5% (154/158), which showws that the diagnosed rate of the combined detection was significantly higher. The difference was statistically significant (P<0.05). Conclusion Ultrasound combined with 64-slice CT in the diagnosis of complex congenital heart disease can obtain such information as heart defects and sites of abnormal passage, the direction of the abnormal blood vessels, the ectopic opening of coronary artery and pulmonary coronary collateral vessels. It can well show the condition of disease, with relatively higher accuracy, which is of great clinical reference value.