To reveal brain 3D microstructures noninvasively and microscopically using MRI, we developed “ex vivo MEMRI” and Mn-Gd double-contrast methods, and then compared them with conventional ex vivo Gd-DTPA-doped contrast. Because MEMRI sample loses contrast after perfusion fixation, we examined the stability of Mn2+ accumulation in ex vivo tissue samples. In addition, we tried to improve the contrast of MEMRI in combination with Gd-DTPA. The Mn-Gd double-contrast showed novel contrast and improved visibility. The functional “MRI staining” methods we developed in this study will be useful for visualizing whole brain 3D microstructures with a higher throughput compared to histological staining.