At SPring-8, synchrotron radiation-based X-ray phase-contrast tomography (PCXI) has been developed to measure the inner structures of biological soft tissue without destroying them. To resolve the three-dimensional (3D) morphology, we have applied PCXI to various cardiovascular tissue samples, including the thoracic aorta, ductus arteriosus, and cardiac conduction system. In the aortic walls, PCXI demonstrated differences in 3D structures of tunica media of aortic dissection. These findings correlated well with the irregularity of the structure of the media. In the surgically excised sample of coarctation of the aorta, PCXI showed 3D morphological changes in transition from the ductus arteriosus to the descending aorta. PCXI is also useful for examining abnormalities of the cardiac conduction system in congenital heart defects. Synchrotron radiation-based X-ray phase-contrast tomography has strong modality for analyzing 3D morphology and is useful for understanding the pathophysiology of various cardiovascular surgical pathologies.