To explore the accuracy of main pulmonary artery (MPA) and ascending aorta (AAO) image evaluation in pediatric patients with single ventricle (SV) by comparing dual-source computed tomography (DSCT) with echocardiography. Thirty-one children with SV were retrospectively enrolled. The stenosis, dilation, and location of MPA and AAO were independently evaluated by DSCT and echocardiography. The accompanying arterial malformations were also assessed by DSCT. For 17 patients undergoing cardiac catheterization, the DSCT-based diameters of MPA and AAO were correlated with their pressures as measured by catheterization. Referring to the surgical and catheterization findings, DSCT had better diagnostic performance in detecting the stenosis, dilation, and location of MPA and AAO with higher sensitivity than echocardiography (sensitivity, MPA: 88.0% vs. 80.0%, AAO: 100% vs. 66.7%, great arteries location: 95.7% vs. 95.2%). The correlations between diameters of MPA and AAO with their pressures were 0.399 (p = 0.04) and 0.611 (p = 0.01), respectively. In addition, DSCT detected 23 cases with patent ductus arteriosus, 26 systemic-to-pulmonary collaterals, 9 branch pulmonary distortions, and 4 coronary artery anomalies. DSCT is reliable for assessing the anatomic features of pulmonary artery and aorta in SV children, and provides comprehensive information for surgical strategy-making.