Resting-state functional magnetic resonance imaging (RS-fMRI) has been proved to be a useful tool to study the brain mechanism in the quest to probe the distinct pattern of inter-region interactions in the brain. As an important application of RS-fMRI, the graph-based approach characterizes the brain as a complex network. However, the network is susceptible to its scale that determines the trade-off between sensitivity and anatomical variability.To balance sensitivity and anatomical variability, a pyramid representation of the functional network is proposed, which is composed of five individual networks reconstructed at multiple scales.The pyramid representation of the functional network was applied to two groups of participants, including patients with Alzheimer's disease (AD) and normal elderly (NC) individuals, as a demonstration. Features were extracted from the multi-scale networks and were evaluated with their inter-group differences between AD and NC, as well as the discriminative power in recognizing AD. Moreover, the proposed method was also validated by another dataset from people with autism.The different features reflect the highest sensitivity to distinguish AD at different scales. In addition, the combined features have higher accuracy than any single scale-based feature. These findings highlight the potential use of multi-scale features as markers of the disrupted topological organization in AD networks.We believe that multi-scale metrics could provide a more comprehensive characterization of the functional network and thus provide a promising solution for representing the underlying functional mechanism in the human brain on a multi-scale basis.© The Author(s) 2022. Published by Oxford University Press on behalf of West China School of Medicine/West China Hospital (WCSM/WCH) of Sichuan University.