This study aimed to comprehensively investigate the neuroanatomical alterations associated with idiopathic Ménière's disease (MD) using voxel-based morphometry and surface-based morphometry techniques. The primary objective was to explore nuanced changes in gray matter volume, cortical thickness, fractal dimension, gyrification index, and sulcal depth in MD patients compared with healthy controls (HC). Additionally, we sought to develop a machine learning classification model utilizing these neuroimaging features to effectively discriminate between MD patients and HC. A total of 55 patients diagnosed with unilateral MD and 70 HC were enrolled in this study. Voxel-based morphometry and surface-based morphometry were employed to analyze neuroimaging data and identify structural differences between the two groups. The selected neuroimaging features were used to build a machine learning classification model for distinguishing MD patients from HC. Our analysis revealed significant reductions in gray matter volume in MD patients, particularly in frontal and cingulate gyri. Distinctive patterns of alterations in cortical thickness were observed in brain regions associated with emotional processing and sensory integration. Notably, the machine learning classification model achieved an impressive accuracy of 84% in distinguishing MD patients from HC. The model's precision and recall for MD and HC demonstrated robust performance, resulting in balanced F1-scores. Receiver operating characteristic curve analysis further confirmed the discriminative power of the model, supported by an area under the curve value of 0.92. This comprehensive investigation sheds light on the intricate neuroanatomical alterations in MD. The observed gray matter volume reductions and distinct cortical thickness patterns emphasize the disease's impact on neural structure. The high accuracy of our machine learning classification model underscores its diagnostic potential, providing a promising avenue for identifying MD patients. These findings contribute to our understanding of MD's neural underpinnings and offer insights for further research exploring the functional implications of structural changes.