Diffusion tensor imaging (DTI) is a new technology in magnetic resonance imaging, which allows us to observe the insightful structure of the human body in vivo and non-invasively. It identifies the microstructure of white matter (WM) connectivity by estimating the movement of water molecules at each voxel. This makes possible the identification of the damage to WM integrity caused by Alzheimer’s disease (AD) at its early stage, called mild cognitive impairment (MCI). Furthermore, the brain’s gray matter (GM) atrophy characterizes the main structural changes in AD, which can be sensitively detected by structural MRI (sMRI) modality. In this research, we further develop a novel multi-modality MRI (DTI and sMRI) fusion strategy to detect WM alterations and GM atrophy in AD patients. The latter is based on a 2- dimensional deep convolutional neural network (CNN) features extractor and a Support Vector Machine (SVM) classifier. The fusion framework consists of merging features extracted from DTI scalar metrics (fractional anisotropy (FA) and mean diffusivity (MD)), and GM using 2D-CNN and feeding them to SVM to classify AD vs. cognitively normal (CN), AD vs. MCI, and MCI vs. CN. Our novel multimodal AD method demonstrates a superior performance with an accuracy of 99.79%, 99.6%, and 97.00% for AD/CN, AD/MCI, and MCI/CN respectively.