Computed tomography combined with angiography has recently been developed to visualize three-dimensional (3D) vascular structure in experimental and clinical studies. However, there remain difficulties in using conventional x-ray angiography to detect small vessels with a diameter less than 200 μm. This study attempted to develop a novel method for visualizing the micro-angioarchitecture of rat spinal cord. Herein, synchrotron radiation-based x-ray in-line phase contrast computed tomography (IL-XPCT) was used to obtain 3D micro-vessel structure without angiography. The digital phase contrast images were compared with conventional histological sections. Our results clearly demonstrated that the resolution limit of the spatial blood supply network in the normal rat thoracic cord appeared to be as small as ~10 μm. The rendered images were consistent with that obtained from histomorphology sections. In summary, IL-XPCT is a potential tool to investigate the 3D neurovascular morphology of the rat spinal cord without the use of contrast agents, and it could help to evaluate the validity of the pro- or anti-angiogenesis therapeutic strategies on microvasculature repair or regeneration.