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Abstract Background Adolescent major depressive disorder (AMDD) is a prevalent and heterogeneous psychiatric condition that emerges during a critical period of brain development. Neuroimaging-based biomarkers derived from resting-state functional magnetic resonance imaging (rs-fMRI) hold promise for objective diagnosis; however, pronounced inter-individual variability and limited sample sizes pose major challenges for robust model development. Methods We propose a memory-augmented Meta-Graph Convolutional Network (BrainMetaGCN) to classify AMDD using rs-fMRI functional connectivity. Individual functional connectivity matrices were constructed by parcellating rs-fMRI time series into cortical regions of interest and computing pairwise correlations. A meta-graph generator dynamically learned subject-specific graph structures, which were processed by lightweight graph convolutional layers. A memory neural network was incorporated to encode population-level prototypical connectivity patterns and generate individualized representations via attention-based retrieval. Model performance was evaluated across multiple independent datasets and compared with state-of-the-art deep learning approaches. Additionally, network interpretability was examined through cortical hierarchy analysis and functional enrichment of discriminative network components. Results The proposed BrainMetaGCN consistently outperformed baseline models, including convolutional and transformer-based approaches, achieving higher accuracy, area under the receiver operating characteristic curve, sensitivity, and specificity. Memory-module–derived functional networks exhibited clear modular organization and showed a significant positive correlation with cortical functional hierarchy, supporting their neurobiological validity. Functional enrichment analyses implicated synaptic transmission, axon guidance, receptor tyrosine kinase signaling, and immune-related pathways, suggesting neurodevelopmental and neuroimmune mechanisms underlying AMDD. Ablation analyses confirmed that memory augmentation and dynamic meta-graph construction were critical for robust performance under small-sample conditions. Conclusions This study introduces a robust and interpretable memory-augmented graph learning framework for AMDD classification. By effectively balancing individual specificity and population-level generalization, BrainMetaGCN advances neuroimaging-based precision diagnosis and provides new insights into the neural and biological mechanisms of adolescent depression.