Voxel-based morphometry method (VBM) has been widely applied to detect the brain atrophy and achieved promising results; however, the effect of the segmentation step in VBM is not clear and the new segmentation method in SPM8 hasn’t been used in Alzheimer’s disease (AD) studies. The aim of this study is to investigate the locations and degrees of grey matter (GM), white matter (WM) atrophy and evaluate the results derived from two segmentation methods. Magnetic resonance imaging (MRI) was collected in 16 AD patients and 16 healthy controls (HC). Using two segmentation methods respectively, several reduction clusters of GM and WM were detected but the locations and degrees of reduction volumes were discrepant resulted from different segmentation methods. Our results suggest that VBM is an effective tool to analyze AD brain atrophy and based on VBM, the comparison of the locations and degrees of volume reduction among AD researches through different segmentation methods should be cautious.