Alzheimer’s disease (AD) is an irreversible neurodegenerative disorder that can lead to progressive memory loss and cognition impairment. Therefore, diagnosing AD during the risk stage, a.k.a. Mild Cognitive Impairment (MCI), has attracted ever increasing interest. Besides the automated diagnosis of MCI, it is important to provide physicians with related MCI cases with visually similar imaging data for case-based reasoning or evidence-based medicine in clinical practices. To this end, we propose a multi-graph learning based medical image retrieval technique for MCI diagnostic assistance. Our method is comprised of two stages, the query category prediction and ranking. In the first stage, the query is formulated into a multi-graph structure with a set of selected subjects in the database to learn the relevance between the query subject and the existing subject categories through learning the multi-graph combination weights. This predicts the category that the query belongs to, based on which a set of subjects in the database are selected as candidate retrieval results. In the second stage, the relationship between these candidates and the query is further learned with a new multi-graph, which is used to rank the candidates. The returned subjects can be demonstrated to physicians as reference cases for MCI diagnosing. We evaluated the proposed method on a cohort of 60 consecutive MCI subjects and 350 normal controls with MRI data under three imaging parameters: T1 weighted imaging (T1), Diffusion Tensor Imaging (DTI) and Arterial Spin Labeling (ASL). The proposed method can achieve average 3.45 relevant samples in top 5 returned results, which significantly outperforms the baseline methods compared.