Objective To detect the value of Dixon in evaluating early optic nerve changes in the patients with thyroid-associated ophthalmopathy (TAO). Methods The clinical and imaging data of 28 consecutive TAO patients and 15 healthy controls were retrospectively analyzed. Signal intensity ratio (SIR), water fraction (WF) of optic nerve and visual acuity were collected and compared between TAO and healthy groups. The correlations between the SIR and WF value of optic nerve and clinical indicators were analyzed using Spearman’s correlation analysis. Receiver operating characteristic curve analysis was applied to assess the discriminating performance of SIR and WF value. Results TAO group had significantly lower visual acuity and higher SIR and WF values of optic nerve than those of healthy group (P < 0.05). SIR and WF value of optic nerve correlated positively with clinical activity score (r = 0.369, P = 0.005; r = 0.420, P = 0.001). Setting a cut-off WF value of 0.914 enabled optimal efficiency and specificity for discriminating optic nerves between TAOs and HCs (area under curve, 0.694; sensitivity, 35.7%; specificity, 93.3%). Combining SIR and WF values of optic nerves, discriminating efficiency and sensitivity were further improved (area under curve, 0.729; sensitivity, 75.0%; specificity, 63.3%). Conclusion Dixon technique is suggested to be used in the evaluation of early optic nerve changes in TAO patients.