Abstract: The rat model of cerebral ischemia with reperfusion was employed to observe intravital microvessels and to measure the fluorescence intensitics of blood, brain and other five internal organs of the body for studying the permeability of cerebral microvessels with fluorescent tracer FLNa. It was designed to find the effect and inherent law of ischemia with reperfusion to the permeability of cerebral microvessels. Experiment results show that ischemia and ischemia with reperfusion do harm to endothelial cells of the capillary; in this case the permeability was obviously enhanced compared with that in normal condition, and the long duration of reperfusion plays roles in repairing trauma. Under the same conditions, their different fluorescence intensities show that their resistance to ischemia and lacking of oxygen isn't identical, the degree of harm vanes, considerably in internal organs, where the most serious is the endothelial cells of liver and kidney, the lesser those of brain and spleen. The condition of lung is an exception and the specialty of lung is related to its structure.