Background Real-time three-dimensional echocardiography (RT-3DE) has made revolutionized improvements of cardiac imaging during the past few years. However, there is no standard examination method for RT-3DE so far. This study aimed to establish the diagnostic method of RT-3DE and evaluate its application in the diagnosis of complex congenital heart diseases (CHD).Methods Fifty patients with complex CHD were examined by RT-3DE with modes of Live 3DE and Full Volume. A series of novel volumetric views combined with Van Praagh sequential segmental approach were introduced to reveal the pathological morphology of the hearts, which were compared with the findings of two-dimensional echocardiography (2DE), angiography and cardiac surgery.Results In 50 patients, 190 image acquisitions of Full Volume were performed at several acoustic windows including subcostal, apical and parasternal regions. Among them, 94.2% (179/190) of image acquisitions were successful. Most sectional volumetric views could be clearly displayed in 92.6% of the successful image acquisitions. However, sectional volumetric views could not be clearly displayed in 7.4%, which was mainly due to poor perspective conditions of examination location, improper instrument multi-parameter setting and insufficient information of whole heart captured in Full Volume acquisitions. As compared with surgical findings and angiography, RT-3DE made correction to the diagnoses in 2 cases including 1 with corrected transposition of the great arteries and the other with single atrium and mitral cleft. The diagnoses initially made by 2DE for these 2 patients were double outlet right ventricle with transposition of the great arteries and complete atrio-ventricular septal defect.Conclusions RT-3DE can clearly display the pathological morphology of complex CHD by a series of novel volumetric views combined with sequential segmental approach through providing more spatial informative cardiovascular structures, which provides a practical method for RT-3DE diagnosis.