A BOLD-based tracking technique was applied to 11 mice to investigate the cerebral circulation. Mapping of the phase of low-frequency component, which is called as “BOLD-based lag structure” showed the typical vascular structure as previous study. Interestingly, BOLD-based lag structure in bilateral somatosensory cortex was similar with the resting state functional connectivity between the bilateral somatosensory cortex. These results indicate the feasibility of this technique in mouse model. Furthermore, our results implies the partial contamination of circulating blood flow in resting state functional connectivity in mouse model.