To explore the differences in gray matter volume and cortical thickness between patients with amnestic mild cognitive impairment (aMCI) and Alzheimer’s disease (AD) and normal elderly individuals, analyzing their relationship with cognitive level, and providing a basis for clinical diagnosis of aMCI and early AD. Methods: 23 aMCI patients, 22 AD patients, and 23 healthy control (NC) groups were prospectively included. Structural MRI (sMRI) scans of brain structures were performed on all subjects. The segment function of CAT12 was used to perform voxel based morphology (VBM) and surface based morphology (SBM) measurements on 3D-T1 MRI images, obtaining the gray matter volume and cortical thickness of specific brain regions for all subjects. Cognitive function assessment was conducted using neuropsychological scales. Analyze the differences in main structural gray matter volume and cortical thickness among three groups, extract regions of interest (ROI) from different brain regions, and investigate their correlation with cognitive scale scores. Results: There are differences in multiple brain regions among the three groups (FWE correction, P<0.05), and the volume of different brain regions is significantly correlated with the Montreal Cognitive Assessment (MoCA) scale scores (P<0.05). Moreover, the magnitude of correlation between the volume of different brain regions and cognitive domains varies significantly (P<0.05). Conclusion: There is a reduction in the uneven distribution of gray matter volume and cerebral cortex in patients with aMCI and AD. The early atrophy of the left hippocampus, olfactory cortex, and insula may be a factor affecting early cognitive function in AD patients.