Meige Syndrome (MS) is a form of segmental dystonia, categorized into four subtypes. The common and specific neuro-mechanisms among these subtypes remain to be elucidated. Herein, 3D T1-weighted MRI images were obtained from 159 patients with primary MS (31 with MS-I, 92 with MS-II, and 36 with MS-IV). Voxel-based morphometry (VBM), surface-based morphometry (SBM), and causal structural covariance network (CaSCN) were utilized to investigate morphological variations and causal relationships in structural changes across subtypes. The study revealed a decremental trend in gray matter volume (GMV) of the right precentral gyrus (PreCG.R), right calcarine cortex (CAL.R), left parietal association cortex (PAL.L), and left hippocampus (HIP.L) from MS-I to MS-IV, which negatively correlated with BFMDRS scores. The progression of GMV atrophy was followed by a trajectory from HIP.L to PAL.L with disease duration and from PAL.R to HIP.L/CAL.L/PreCG.R with increasing BFMDRS scores. Support vector machine (SVM) analysis indicated that these GMV changes might be served as potential biomarkers for diagnosing MS subtypes, with areas under the curve (AUC) of 0.935, 0.864, and 0.882, respectively. The results suggest that the PreCG.R is a key region affected early in MS, with GMV reductions extending to other brain areas as the disease progresses, indicating a hierarchy of structural brain changes associated with disease duration in MS progression. Our study further provides evidence for the association of MS with extensive gray matter abnormalities.