For the precise preoperative evaluation of complex congenital heart diseases (CHDs) with reduced radiation dose exposure, we assessed the diagnostic validity and reliability of low-dose prospective ECG-gated cardiac CT (CCT). Forty-two individuals with complex CHDs who underwent preoperative CCT as part of a prospective study were included. Each CCT image was examined independently by two radiologists. The primary reference for assessing the diagnostic validity of the CCT was the post-operative data. Infants and neonates were the most common age group suffering from complex CHDs. The mean volume of the CT dose index was 1.44 ± 0.47 mGy, the mean value of the dose-length product was 14.13 ± 5.4 mGy*cm, and the mean value of the effective radiation dose was 0.58 ± 0.13 mSv. The sensitivity, specificity, PPV, NPV, and accuracy of the low-dose prospective ECG-gated CCT for identifying complex CHDs were 95.6%, 98%, 97%, 97%, and 97% for reader 1 and 92.6%, 97%, 95.5%, 95.1%, and 95.2% for reader 2, respectively. The overall inter-reader agreement for interpreting the cardiac CCTs was good (κ = 0.74). According to the results of our investigation, low-dose prospective ECG-gated CCT is a useful and trustworthy method for assessing coronary arteries and making a precise preoperative diagnosis of complex CHDs.