Objective To study the diagnostic value and clinical application effects of dualsource computed tomography (DSCT) and transthoracic echocardiography (TTE) for complex congenital heart disease (CCHD). Methods The clinical data of 109 patients with CCHD in our hospital from June 2016 to June 2018 were retrospectively analyzed. The surgical results were used as the gold standard to analyze the examination results of DSCT and TTE in CCHD patients and the diagnostic accuracy rates of two examination methods in the diagnosis of cardiac malformation, macrovascular malformation and all malformation. Results A total of 241 malformations were confirmed by surgery in 109 CCHD patients, including 115 cardiac malformations (47.72%) and 126 macrovascular malformations (52.28%). The accuracy rates of DSCT and TTE were 86.96% and 94.78% for cardiac malformation (P<0.05), and there were 15 missed diagnosis and misdiagnosis by DSCT, including 4 atrial septal defect, 3 ventricular septal defect, 2 aortic stenosis with regurgitation, 2 pulmonary valve stenosis, 2 ventricular reversal, 1 single atrium and 1 mitral atresia. There 6 misdiagnosis and missed diagnosis by TTE, including 2 ventricular septal defect, 1 atrial septal defect, 1 single atrium and 1 single ventricle. The accuracy rates of DSCT and TTE were 92.86% and 72.22% for macrovascular malformation (P<0.05), and there were 10 missed diagnosis and misdiagnosis by DSCT, including 3 patent ductus arteriosus, 2 pulmonary orifice stenosis, 2 pulmonary venous anomalous drainage, 1 permanent left upper chamber and 1 transposition of great artery. There were 35 misdiagnosis and missed diagnosis by TTE, including 6 aortic overriding, 5 patent ductus arteriosus, 5 transposition of great arteries, 4 pulmonary orifice stenosis, 4 permanent upper left ventricle, 3 pulmonary venous anomalous drainage, 3 transverse aortic constriction, 3 main pulmonary artery collateral formation and 2 pulmonary atresia. And the accuracy rates of two methods for CCHD were 90.04% and 82.99% (P<0.05). Conclusion The accuracy rate of DSCT in the diagnosis of cardiac malformation is inferior to that of TTE, and its accuracy rate in the diagnosis of macrovascular malformation is better than that of TTE. The combination of two examinations can effectively improve the accuracy and safety of CCHD diagnosis.