Purpose To compare the diagnostic accuracy of peripapillary retinal nerve fiber layer with macular ganglion cell complex thickness as an auxiliary tool for the early diagnosis of dysthyroid optic neuropathy and help assess the effectiveness of the treatment. Methods In this retrospective case-control study, a total of 58 thyroid-associated opthalmopathy patients and 58 healthy participants were enrolled in the study. Thyroid-associated opthalmopathy patients were divided according to the European Group Graves' Orbitopathy severity classification. The thicknesses of peripapillary nerve fiber layer and macular ganglion cell complex were measured using optical coherence tomography and their correlation with the severity of the disease as well as the effect of the treatment was investigated. Results No statistically significant differences were found between the mild thyroid-associated opthalmopathy group and the control group in both peripapillary nerve fiber layer and macular ganglion cell complex thickness. In the moderate-to-severe thyroid-associated opthalmopathy group, however, Temporal and Nasal peripapillary nerve fiber layer thicknesses were lower compared to the control group (p = 0.041, p = 0.012), whereas in the sight-threatening thyroid-associated opthalmopathy group Temporal Inferior, Nasal Superior, and mean (G) peripapillary nerve fiber layer thicknesses were larger (p = 0.000, p = 0.004, p = 0.000). No significant differences were observed in the macular ganglion cell complex thickness among the different severity groups and the control groups (p > 0.05). After treatment, the mean peripapillary nerve fiber layer thickness decreased whereas mean macular ganglion cell complex thickness showed no significant change in the sight-threatening group. A correlation was established between exophthalmos, best corrected visual acuity, clinical activity score, disease course, and the mean peripapillary nerve fiber layer thickness. The area under curve analysis indicated that mean peripapillary nerve fiber layer thickness can be used as a powerful diagnostic tool in early stage dysthyroid optic neuropathy in thyroid-associated opthalmopathy patients. Conclusion Our study indicates that peripapillary nerve fiber layer act as an auxiliary tool for the early diagnosis of dysthyroid optic neuropathy and helps assess the effectiveness of the treatment.