Abstract: Three-dimensional ultrasound microvascular imaging is helpful for the diagnosis of cerebrovascular diseases. In this paper, ultrafast ultrasound imaging, ultrafast ultrasound power Doppler and mechanical scanning were combined to perform three-dimensional imaging of cerebrovascular and evaluation of cerebral ischemic status. The ultrafast data acquisition sequence and 3D scanning system with the capability of high-speed acquisition and compression storage, were developed. GPU based algorithm was carried out for efficient beamforming. Furthermore, based on SVD clutter filtering, dynamic signals of small vessel were extracted from 3D ultrasound data, and power Doppler images of each slice and color Doppler imaging of small vessels in coronal plane were obtained. Finally, the 3D image was obtained using a voxel-based reconstruction method. Results of a rat brain showed that such an imaging system can be used for in vivo imaging of three-dimensional cerebral vascular networks, as well as quantitative evaluation of cerebral vascular injury. This work can benefit for the development of new methods for encephalopathy detection and diagnosis. In addition, the method and systems in present study can be helpful for microvascular imaging of other tissues.