Imaging brain microvasculature is important in plasticity studies of cerebrovascular diseases. Applying contrast agents, traditional μCT and μMRI methods gain imaging contrast for vasculature. The aim of this study is to develop a synchrotron radiation X-ray inline phase-contrast tomography (SRXPCT) method for imaging the intact mouse brain (micro)vasculature in high resolution (~3.7 μm) without contrast agent. A specific preparation protocol was proposed to enhance the phase contrast of brain vasculature by using density difference over gas-tissue interface. The CT imaging system was developed and optimized to obtain 3D brain vasculature of adult male C57BL/6 mice. The SRXPCT method was further applied to investigate the microvasculature changes in mouse brains (n = 14) after 14-day reperfusion from transient middle cerebral artery occlusion (tMCAO). 3D reconstructions of brain microvasculature demonstrated that the branching radius ratio (post- to preinjury) of small vessels (radius < 7.4 μm) in the injury group was significantly smaller than that in the sham group (p < 0.05). This result revealed the active angiogenesis in the recovery brain after stroke. As a high-resolution and contrast-agent-free method, the SRXPCT method demonstrates higher potential in investigations of functional plasticity in cerebrovascular diseases.