Objective To analyze the diagnostic value of dual-phase three-dimensional steady-state precession (3D SSFP) in large vessels malformations of congenital heart disease(CHD). Methods A total of 46 cases of patients with congenital heart disease (CHD) diagnosed by ultrasound in our hospital in the past two years (December 2015 to December 2017) were treated with chest dual-phase 3D SSFP imaging and traditional contrast enhanced magnetic resonance angiography (CE-MRA) technique before or after surgery. The large vessels image quality and measured large vessels diameters of CHD patients were compared between the two MR examinations, and the diagnostic efficacy of dual-phase 3D SSFP imaging in large vessels malformations of CHD was analyzed and evaluated. Results There was no significant difference in the large vessels image quality in CHD patients between the two MR examinations (P>0.05). There were significant differences in the diameters of aorta, left pulmonary artery and right pulmonary artery measured by 3D SSFP in systolic phase and diastolic phase and CE-MRA (P<0.05), and there was no significant difference in the diameters of common pulmonary artery and inferior vena cava (P>0.05). The diameters of aorta, common pulmonary artery and right pulmonary artery measured by 3D SSFP in systolic phase were significantly larger than those in diastolic phase (P<0.05), and there was no significant difference in the diameter of left pulmonary artery and inferior vena cava compared with those in diastolic phase (P>0.05). Conclusion 3D SSFP imaging can be used to the diagnosis of large vessels morphology of patients with congenital heart disease, and can measure the diameters of large vessels in different cardiac phases accurately, and it helps to develop a reasonable treatment regimen and improve the treatment effects of CHD patients.