Alzheimer’s Disease （AD） is a progressive neurodegenerative disease with hidden causes， and can result in structural changes of patients’ brain regions. For assisting the doctors to make correct judgment on the condition of AD patients， an improved Three-Dimensional Principal Component Analysis Network （3DPCANet） model was proposed to classify AD by combining the mean Amplitude of Low-Frequency Fluctuation （mALFF） image of the whole brain of the subject. Firstly， functional Magnetic Resonance Imaging （fMRI） data were preprocessed， and the mALFF image of the whole brain was calculated. Then， the improved 3DPCANet deep learning model was used for feature extraction. Finally， Support Vector Machine （SVM） was used to classify features of AD patients with different stages. Experimental results show that the proposed model is simple and robust， and has the classification accuracies on Subjective Memory Decline （SMD） vs. AD， SMD vs. Late Mild Cognitive Impairment （LMCI）， and LMCI vs. AD reached 92.42%， 91.80% and 89.33% respectively， which verifies the effectiveness and feasibility of the proposed method.