To investigate the clinical significance of the application of 320-row CT angiography with low-dose prospective ECG-triggered target scanning in children with complex congenital heart disease (CHD), and to compare with the results from transthoracic echocardiography (TTE). 22 patients (male 12 cases, female 10 cases, average age: 18 months, range: 14 days-9 years, average weight: 13 kg) received an examination through 320-row CT angiography with low-dose prospective ECG-triggered volume target scan mode and transthoracic echocardiography. The center of phase window for data collection in this study was set to 40% of the R-R interval. Of these, 18 patients received surgery and 4 patients received conventional cardiac angiography (CCA). The diagnostic accuracy of 320-row CTA was calculated according to the examination results from surgical and/or cardiac angiography. The overall quality score for CTA images was divided into five levels. The results were compared with the research data of radiation doses obtained from patients with congenital heart disease who had received CT angiography. Complex congenital heart disease was confirmed by surgical or CCA in each of 22 patients, with 42 cases of large vascular malformations outside the heart cavity, and 26 of intracardiac malformations. The diagnostic accuracy of 320-row CT angiography and transthoracic echocardiography for large vascular malformation outside the heart cavity was 95.2 and 80.9%, respectively; for intracardiac malformation the accuracy was 88.5 and 100.0%, respectively. There was significant difference between 320-row CT and transthoracic echocardiography in the diagnosis of large vascular malformation outside the heart cavity (P < 0.05) with better results in 320-row CT, and no significant difference was found in the diagnosis of intracardiac malformation (P > 0.05). The average subjective image quality score was 4.4 ± 0.7 points. The average effective dose was 0.42 ± 0.08 mSv. 320-row CT enables direct visualization of the vascular configuration and shape of the aorta, pulmonary artery, and other large vessels to diagnose extracardiac vascular malformations. Combined with transthoracic echocardiography, 320-row CT is a promising technology that may be able to replace catheter based angiography to evaluate congenital cardiovascular malformations.