Rac1 is critical for synapse remodeling. In this work, we investigated whether Rac1 could induce neuroimaging changes in a transgenic mouse model using structural MRI, resting state-fMRI and MRS at 11.7T. Our data showed that the volume of the medial prefrontal cortex (mPFC) is significantly decreased in Rac1 activation group. Moreover, we found that the upregulation of Rac1 activity is related to increased functional connectivity in mouse brain. However, Glx or GABA levels do not show significant changes in mPFC. We concluded that the upregulation of Rac1 activity is related to structural and functional neuroimaging changes.