OBJECTIVES: The current study aimed to investigate the structural and functional connectivity of the subregions of the amygdala in children with Attention Deficit/Hyperactivity Disorder (ADHD) only or comorbid with Oppositional Defiant Disorder (ODD). METHODS: A total of 354 children with ADHD-only, 161 children with ADHD and ODD (ADHD + ODD), and 100 healthy controls were enrolled. The Child Behavior Checklist (CBCL) and the Behavior Rating Inventory of Executive Function (BRIEF) were filled out by caregivers. Analysis of covariance (ANCOVA) was performed to test group-wise differences in these behavioral measures. A subsample comprising 209 participants underwent a resting-state functional MRI scan and a diffusion-weighted imaging (DWI) scan. Functional connectivity and structural connectivity were calculated using bilateral subregions of the Amygdala as seeds. Between-group voxel-wise comparisons were conducted. RESULTS: The ADHD + ODD group had more anxious/depressed moods, more delinquent and aggressive behaviors, more emotional control problems, and more inhibition deficits than the ADHD-only group (all P CONCLUSIONS: Altered structural and functional connectivity of the subregions of the amygdala in children with ADHD compared with their healthy counterparts were respectively associated with ADHD-related behavioral and emotional problems. CLINICAL TRIAL NUMBER: not applicable.