Voxel-based morphometry (VBM) is widely used to diagnose Alzheimer’s disease (AD). Recently, several studies have showed that quantitative susceptibility mapping (QSM) is also useful for detecting iron deposition in the early stages of AD. In this study, we propose a novel diagnosis index for AD based on both QSM and VBM, which are simultaneously executed by a single scan. The diagnostic performance of the proposed index in regard to AD and MCI patients is compared with that of the conventional VBM-based index. The comparison results show that the proposed index improved diagnostic performance for discriminating MCI patients and control groups.