Dual phase whole heart imaging allows accurate depiction of cardiac segmental anatomy for congenital heart disease. We applied image-based navigation (iNAV) to improve its clinical utility. Qualitative and quantitative image quality scoring showed that iNAV gave equivalent image quality compared to the standard respiratory navigator. However, the distal coronary arteries were better visualized and the sequence duration was shorter. Using dual-phase iNAV, complete segmental anatomy was delineated in 27/30 patients (90%). The use of iNAV dual phase 3D SSFP whole heart acquisition allows complete morphological diagnosis for congenital heart disease with high image quality with more clinically acceptable time constraints.