A transcranial Doppler-based method for displaying 3D intracranial blood flow information and a system thereof, comprising: A. performing multi-beam ultrasound scanning on predetermined intracranial areas using transcranial Doppler ultrasound probe, receiving ultrasonic echo signals B. calculating, on basis of ultrasonic echo signal, to obtain blood flow information C. obtaining blood flow information in a plurality of directions on basis of scanning of predetermined areas, forming stereoscopic models including blood flow information D. visualizing data of stereoscopic model to form 3D images, and performing individualized adjustments to 3D images according to user commands, and outputting images and presenting to user. Compared with MRI, CT, DSA and the like, present invention is low-cost, convenient and capable of repeated detection. Present invention can significantly reduce degree of reliance on an operators experience, provide blood flow information more complete and objective.