The Alzheimer's Disease (AD) usually leads to atrophy of hippocampus region. According to the characteristic, a Convolutional Neural Network (CNN) based method was proposed for the diagnosis of AD by using the hippocampu region in brain Magnetic Resonance Imaging (MRI). All the test data were got from the ADNI database including 188 AD and 229 Normal Control (NC). Firstly, all the brain MRI were preprocessed by skull stripping and aligned to a template space. Secondly, a linear regression model was used for age correction of brain aging atrophy. Then, after preprocessing, multiple 2.5D images were extracted from the hippocampus region in the 3D brain image for each object. Finally, the CNN was used to train and recognize the extracted 2.5D images, and the recognition results of the same object were used for the joint diagnosis of AD. The experiments were carried out by using multiple ten-fold cross validation methods. The experimental results show that the average recognition accuracy of the proposed method reaches 88.02%. The comparison results show that, compared with Stacked Auto-Encoder (SAE) method, the proposed method has improved the diagnosis effect of AD in the case of only using MRI.