To identify the structural and functional abnormalities in mild cognitive impairment (MCI) amyloid positive patients, combined resting state fMRI (rs-fMRI) and diffusion kurtosis imaging (DKI) were applied in this study. Graph theory metrics of subgroups were calculated and compared. In the results, MCI amyloid positive had impaired structural connectivity (SC) but not functional connectivity (FC) matrices and demonstrated significant SC-FC decoupling. We postulated that structural damage preceded functional reorganization. The pathological effects of fibrillar amyloid plaque toxicity occur in anatomical pathways, and functional reorganization might happen beyond the confines of structural pathways.