Hemifacial spasm (HFS) is characterized by unilateral and paroxysmal contraction of orofacial muscles. A group of HFS patients and healthy controls underwent MRI examination and clinical assessment for facial spasm and affective disorders. HFS patients showed thickened left fusiform in cortex along with reduced subcortical volume in the right amygdala. Increased amygdala-driven connections were revealed to the bilateral superior frontal gyrus (SFG) and orbital gyrus (OG), and increased functional connectivity (FC) was detected of fusiform seed to several subregions of frontal lobe. These altered FC changes were associated with certain clinical indices, providing new insight into pathophysiology of the disease.