Background Discriminating the stage of thyroid-associated ophthalmopathy (TAO) is crucial for the treatment strategy and prognosis prediction. Utility of conventional magnetic resonance imaging in the disease staging is limited. Purpose To investigate the performance of T2 mapping based on different region of interest (ROI) selection methods in the staging of TAO. Material and Methods Thirty-two patients with TAO were retrospectively enrolled. Two radiologists independently measured the T2 relaxation time (T2RT) of extraocular muscles using two different ROIs (hotspot [ROIHS]: T2RT-hot; single-slice [ROISS]: T2RT-mean, T2RT-max, T2RT-min). Independent-samples t test, Wilcoxon signed rank test, Spearman correlation analysis, receiver operating characteristic (ROC) curves analyses, multiple ROC comparisons, and intra-class correlation coefficient (ICC) were used for statistical analyses. Results No significant difference was found in the measuring time between ROIHS and ROISS methods ( P = 0.066). T2RT-mean demonstrated the highest ICC for measurement, followed by T2RT-max and T2RT-min, and T2RT-hot showed the poorest reproducibility. Active TAOs showed significantly higher values for all the T2RTs than inactive mimics (all P < 0.001). Significant positive correlations were found between T2RTs and CAS (all P < 0.005). T2RT-hot and T2RT-max showed significantly higher areas under the curve than that of T2RT-mean ( P = 0.013 and 0.024, respectively), while the difference between T2RT-hot and T2RT-max was not significant ( P = 0.970). Conclusion The T2RTs derived from both ROI selection methods could be useful for the staging of TAO. The results of measuring time, reproducibility, and diagnostic performance suggest that T2RT-max would be the optimal indicator for staging.