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Adverse childhood experiences (ACEs) contribute to over 25% of youth psychiatric disorders, yet neurobiological pathways remain elusive. This large-scale longitudinal study from the ABCD cohort demonstrates that whole-brain functional connectivity modulates the association between ACEs and transdiagnostic mental disorders during the critical transition to adolescence. Notably, this protective effect is specifically pronounced for threat-related ACEs and among female youths, implicating cognitive control networks as key resilience substrates.