The aim of this study was to compare the coronary artery visibility and radiation dose in infants with CHD on cardiac 128-slice CT and on cardiac 64-slice CT. The images of 200 patients were analyzed in this study, 100 patients were selected randomly from a group of 789 infants (<1 years old) with CHD undergoing 128-slice CT prospective ECG-triggered axial scan, and 100 were selected randomly from 911 infants with CHD undergoing 64-slice CT retrospective ECG-gated spiral scan. The visibility of coronary artery segments was graded on a four-point scale. The coronary arteries were considered to be detected or visible when grade was 2 or higher. The visibility of the coronary artery segments and the radiation dose was compared between the two groups. Except for the rate of LM (96 vs. 99 %), the detection rates of the total, LAD, LCX, RCA, and the proximal segment of the RCA in the 256-slice CT group were significantly higher than those in the 64-slice CT group (51.7, 53.33, 33.67, 53.33, and 99 vs. 34.8, 34.33, 18, 30.67, and 75 %, respectively). The counts of visibility score (4/3/2/1) for the LM and the proximal segment of the RCA were 62/22/12/4 and 56/20/17/7, respectively, in the 128-slice CT group and 17/42/30/1 and 9/30/38/25, respectively, in the 64-slice CT group. There were significant differences, especially for score 4 and 3, between the two groups. The radiation dose in the 128-slice CT group was significantly decreased than those in the 64-slice CT group (CTDI_vol 1.88 ± 0.51 vs. 5.61 ± 0.63 mGy; SSDE 4.48 ± 1.15 vs. 13.97 ± 1.52 mGy; effective radiation dose 1.36 ± 0.44 vs. 4.06 ± 0.7 mSv). With reduced radiation dose, the visibility of the coronary artery in infants with CHD via prospective ECG-triggered mode on a 128-slice CT is superior to that of the 64-slice CT using retrospective ECG-gated spiral mode.