Objective To evaluate the low-dose prospective ECG-gated 128-slice spiral CT angiography in the diagnosis of complex congenital heart disease in children. Methods Thirty-five children with congenital heart disease received low-dose prospective ECGgated 128-slice spiral CT angiography, The CT dose index volume(CTDIvol) and dose length product(DLP) were recorded in order to calculate effective(ED). Diagnosis and overall image quality were assessed by two experienced radiologists by using a five point scale independently. The surgical results were taken as the diagnostic standards, and the CT angiography data were compared with UCG results using χ2 test. Results The CTDIvol was(0.90±0.24)mGy. The DLP was (12.9±4.7)mGy·cm. The ED was (0.29±0.09)mSv with a range of 0.156 mSv to 0.52 mSv. The average subjective image quality score was (4.3±0.7). All images were diagnosable. The definitive diagnosis of extracardiac vascular anomalies was made in 97.2%(104/107) of patients by using 128-slice spiral CT angiography, which were significantly superior to UCG results[90.6%(97/107)] (χ2=4.013,P＜0.05). In the cardiac malformations, the definitive diagnosis by 128-slice spiral CT angiography was 98.2%(57/58) and there was no significant difference between 128-slice spiral CT angiography results and UCG results [96.6%(56/58)](χ2=0.342,P ＞0.05). The definitive diagnosis of the cardiac/large-vessel malformations was made in 100％(24/24) of the patients by both 128-slice spiral CT and UCG. The definitive diagnosis of extracardiac vascular anomalies was made in 92.0%(23/25) of patients by using 128-slice spiral CT angiography, which were significantly superior to UCG results[68.0%(17/25)](χ2=4.500, P＜0.05). In addition, 128-slice spiral CT angiography detected airway abnormality in 3 cases. Conclusion The low-dose prospective ECGgated 128-slice spiral CT angiography exhibits great application value in the diagnosis of complex congenital heartdisease, which significantly reduce the radiation dose．