Background: Increasing evidence has indicated that the entire visual pathway from retina to visual cortex may be involved in dysthyroid optic neuropathy (DON) pathological mechanisms. Purpose: To explore the functional and morphological brain characteristics in DON and their relationship with ophthalmologic performance. Study Type: Retrospective. Population: A total of 30 DON patients, 40 thyroid-associated ophthalmopathy (TAO) without DON patients and 21 healthy-controls (HCs). Field Strength/Sequence: A 3.0 T, 3D T1-weighted spoiled gradient-recalled echo and gradient-recalled echo-planar imaging. Assessment: Functional and structural alterations in brain regions were evaluated with fractional amplitude of lowfrequency fluctuations, degree centrality (DC), and gray matter volume (GMV). Clinical activity score (CAS) is assessed across patients. Statistical Test: One-way analysis of variance with post hoc two sample t-tests (GRF-corrected, voxel level: P < 0.005, cluster level: P < 0.05) and correlation analysis (significance level: P < 0.05). Results: Compared to HCs, DON patients had significantly decreased DC values in the bilateral BA17 and BA18 regions. Compared to the TAO group, DON patients had decreased GMV in the left anterior cingulate cortex, left middle frontal gyrus, left lingual gyrus, left parietal gyrus, right Rolandic operculum, left supplementary motor area, and right middle temporal gyrus. In addition, GMV in the right Rolandic operculum was significantly positively correlated with CAS (correlation coefficient: r = 0.448). Data Conclusion: This study showed significant morphological and functional alterations in visual cortex and morphological alterations in partial default mode network regions of DON patients, which may provide insights into the mechanism of vision loss and may facilitate the diagnosis and treatment of DON. Evidence Level: 3. Technical Efficacy: Stage 3.