Facial synkinesis is a disease characterized by unintentional activation of facial muscles, which causes that the patients cannot control their facial expressions independently. Previous studies have shown that its pathogenesis is related to the reorganization of cerebral cortex, but it remains unclear what brain changes the patients have at different stage of the disease. For this study, we recruited 30 patients with facial synkinesis and 19 healthy control subjects from Shanghai Huashan Hospital. All participants completed bilateral blinking and grinning tasks while functional magnetic resonance imaging (fMRI) data was collected. We measured the brain activation strength of each task and observed the activation similarity of the ipsilateral tasks. Then we explored the correlation between activation pattern and clinical scale. Results showed different activation pattern along the courses of disease for blinking and grinning task, which may be due to the inconsistent process of cortical reorganization. The late stage group activated more in blinking task, but the least in grinning tasks, especially on the affected side (p<0.001 at voxel level, p<0.05 at cluster level, FWE corrected). Compared with healthy controls, the activation of patients between tasks on the affected side is more similar(p<0.05). There was a negative correlation in right postcentral gyrus between activation similarity and scale scores (symmetry of voluntary movement scores: R = -0.469, p = 0.009). This could be attributed to the rearrangement of the nervous system following facial nerve injury, leading to incorrect connections between nerves and muscles. Our study may be helpful for understanding mechanism of facial synkinesis and provide basis for the stage-dependent diagnosis and treatment.