Acute spinal cord injury (SCI) always leads to severe destruction of the microvascular networks. To investigate the three-dimensional (3D) alterations of microvasculature following SCI, we utilized an established rat SCI model. Based on the hypothesis that the spinal cord would undergo reorganization and postinjury modification of the vascular networks after SCI, we reconstructed the normal and injured angioarchitecture using micro-CT images of silicone rubber microsphere-perfused specimens. Several morphometric parameters were used to study the 3D vascular alterations in the SCI rat model, including the casting-based vessel volume fraction, connectivity density, separation, thickness and thickness distribution. Our results indicated that the microvascular spatial conformations were significantly different between the normal and injured spinal cord segments. The morphometric changes showed an increase of the vessel volume fraction and separation and a decrease of vessel connectivity density during the vascular healing process after SCI. Our results may contribute to elucidation of the mechanisms of compensatory vascular reconstitution in traumatized spinal cord. The method used here has the potential to improve our understanding of changes in the spatial architecture of vascular networks after SCI compared to the conventional histomorphology techniques. In summary, we developed a new methodology to analyze neurovascular pathology based on 3D vascular network patterns and features in an experimental rat SCI model. This technique could be used as a complementary tool to investigate the efficacy and side effects of therapeutic drugs or rehabilitation regimens.