The identification of subtle brain changes that are associated with mild cognitive impairment (MCI), the at-risk stage of Alzheimer’s disease, is still a challenging task. Different from existing works, which employ multimodal data (e.g., MRI, PET or CSF) to identify MCI subjects from normal elderly controls, we use four MRI sequences, including T1-weighted MRI (T1), Diffusion Tensor Imaging (DTI), Resting-State functional MRI (RS-fMRI) and Arterial Spin Labeling (ASL) perfusion imaging. Since these MRI sequences simultaneously capture various aspects of brain structure and function during clinical routine scan, it simplifies finding the relationship between subjects by incorporating the mutual information among them. To this end, we devise a hypergraph-based semisupervised learning algorithm. In particular, we first construct a hypergraph for each of MRI sequences separately using a star expansion method with both the training and testing data. A centralized learning is then performed to model the optimal relevance between subjects by incorporating mutual information between different MRI sequences. We then combine all centralized hypergraphs by learning the optimal weight of each hypergraph based on the minimum Laplacian. We apply our proposed method on a cohort of 41 consecutive MCI subjects and 63 age-and-gender matched controls with four MRI sequences. Our method achieves at least a 7.61% improvement in classification accuracy compared to state-of-theart methods using multiple MRI data.