This study aims to investigate the image quality and radiation dose of prospective ECG-triggered 128-slice dual-source CT (DSCT) angiography in the delineation of coronary arteries in infants with congenital heart disease (CHD). Sixty-three infants with CHD were randomly assigned into two groups: prospective ECG-triggered sequential protocol (group 1) and high-pitch spiral protocol (group 2). Patients were selected to the protocols randomly. A five-point scoring system was applied to study the capability of detecting coronary arteries. A score of < 3 represents non-diagnostic. Effective radiation dose (ED) was calculated. The visualized rate for original, proximal, middle and distal segments of the coronary arteries was 98%, 95%, 94% and 83%, respectively in group 1, 93%, 82%, 53% and 34%, respectively in group 2. There were no significant demographic differences in the identification rate between the two groups as to the original and most of the proximal segments. Significant demographic differences were found in middle and distal segments (p < 0.05). The mean ED of the high pitch group and the sequential group was 0.33 ± 0.11 mSv and 0.63 ± 0.16 mSv, respectively. Both the prospective ECG-gated high-pitch mode and the sequential mode for 128-slice DSCT allow satisfactory delineation of original and most of the proximal segments of coronary arteries in infants with CHD. However, an ECG-gated sequential mode is recommended when detailed anatomic assessment of the whole coronary arteries are needed since the ECG-gated high-pitch mode is limited in the delineation of middle and distal segments of the coronary arteries.