AIM: To assess changed spontaneous brain activity in hyperthyroid exophthalmos (HE) patients by the amplitude of the low-frequency fluctuation (ALFF) method, and to analyze the correlation between brain activity and ALFF values in these patients. METHODS: Totally 18 HE and 18 hyperthyroid non-exophthalmos (HNE) patients were enrolled. The participants were tested by resting-state functional magnetic resonance imaging, and receiver operating characteristic (ROC) curves were generated to classify the ALFF values of the study population. Pearson’s correlation analysis was utilized to evaluate the relationship between the ALFF values obtained from different brain areas and clinical manifestations. RESULTS: Contrary to HNE patients, we observed lower ALFF values in the left calcarine fissure and surrounding cortex (LCFSC) in HE patients. In the ROC curve analysis of the LCFSC, the area under the curve reflected a high degree of accuracy. In addition, there was positive correlation between mean ALFF values of the LCFSC and the best-corrected visual acuity of the affected eyes. CONCLUSION: The study displays abnormal brain activity in LCFSC in patients with HE, which might suggest pathological mechanism of visual impairment of HE patients.