Magnetic Source Imaging (MSI) is a neural functional imaging technique which combines Magnetic Resonance Imaging with Magnetoencephalography (MEG). Magnetic Source Images merge the brain function with its anatomic structure. Therefore MSI can position the lesions and important functional areas of the brain clearly and accurately. In this paper, we studied and discussed the 3D visualization and quantitative analysis of MSI, especially the 3D distance measurement of the dipoles. MRI volume was segmented and the gray matter was 3D reconstructed using VTK functions. Based on the landmark points (left ear former nest, right ear former nest and nasion) defined before MEG test, the information of dipoles exported from the source analysis software was visualized in the 3D render window after coordinate transformation. The coordinate position of interested dipoles was picked up using VTK tools, and the distance between two dipoles picked was calculated. As a result of 3D visualization, the abnormal discharge sources and important functional brain areas were rendered with the 3D brain model. The distance measurement result met the clinical demand with an average error of 0.2999mm and an average relative error of 0.7816%. © 2011 IEEE.