A process of evaluating blood-brain barrier permeability of a stroke rat by using fluorescent substance is disclosed. This process uses an Evans blue dye having spontaneous fluorescence properties, in combination with the use of a new non-invasive in vivo imaging system (IVIS), to obtain fluorescent signals so as to assess the change in the blood-brain barrier permeability of rodents after a cerebral artery stroke model surgery. In operation, an Evans blue dye is injected into a stroke rat of middle cerebral artery occlusion model. A non-invasive in vivo imaging system is used to detect the fluorescence distribution of the whole brain, and obtain images combined by the fluorescence images and optical images for the whole brain tissue. Thereby, the change in the blood-brain barrier permeability of the stroke rat can be completely realized.