Stroke is a heterogeneous syndrome caused by various diseases resulting from disruption of cerebral blood flow (CBF) and brain tissue necrosis. Ischemic stroke is the major type of this syndrome induced by brain infarction. The infarct area will accompany with cerebral edema which could change the optical properties of the brain tissue. Near infrared spectroscopy (NIRS) was commonly used in measuring the concentration of the main chromophores in the blood oxyand deoxy- hemoglobin for acquiring the hemodynamic or metabolic change in the tissue. In our previous studies, we have shown the hemodynamic activity of stroke rat using frequency domain NIRS (FDNIRS). To precisely locate the ischemic infarct region within whole brain, we develop a noninvasive, diffuse optical imaging (DOI) system based on NIRS. To localize the infarct area and morphological information, the 2D scanning system with DOI technique was developed. The optical properties of the tissue i.e. absorption and scattering coefficient, representing the photon transmission model in the tissue, were applied to observe the structural changes of the brain tissue. In the pilot study, we have applied FDNIRS to monitor the changes of blood oxygen level controlled by neurovascular coupling in ischemic brain. By comparing the FDNIRS measurement result of the sham group with the middle carotid arterial occlusion (MCAO) group stroke rat on post operation day 3. We found that there is a high correlation between the reduced scattering coefficient and the infarct area tissue. The system has been applied to observe the in-vivo experiment of ischemic animal stroke model. Further study can develop optical techniques for monitoring and diagnosing the progress of stroke and the novel therapy methods.