Purpose To perform orbital magnetic resonance imaging (MRI) three-dimensional (3D) reconstruction based on volume rendering and analyse changes in soft tissues in dysthyroid optic neuropathy (DON) patients. Methods Using MRI 3D reconstruction based on volume rendering, orbital model parameters were compared with measurements made by observers. The fat volume (FV) and extraocular rectus muscle volume (EOMV) of subjects were calculated via MRI 3D reconstruction. Visual functions were assessed for all thyroid-associated ophthalmology (TAO) patients. Receiver operating characteristic (ROC) curves were analysed to evaluate DON in soft tissues. Correlations between visual function parameters and 3D reconstruction measurement were analysed. Results All interclass correlation coefficients between the 3D reconstruction and observer measurements were above 0.950. A total of 21 healthy orbits, 38 TAO orbits without DON and 23 TAO orbits with DON were studied. The FV and EOMV were greater in the DON group than in the healthy and non-DON groups (all p < 0.05). EOM enlargement contributed the most to the DON (odds ratio = 2.79, 95% confidence interval = 1.53, 5.07). The areas under the ROC curves of the reconstruction measurements were as follows: EOMV, 0.850; FV, 0.674; whole volume, 0.726; and EOMV/FV, 0.712. Visual function impairment was positively associated with EOM enlargement. When the EOMV was above 4.035 ml, the occurrence of DON was probable. Conclusions MRI 3D reconstruction based on volume rendering is a reliable method for analysing orbital soft tissues. A larger the EOMV was the most relevant factor in DON.