ABSTRACT Background: Emotional dysregulation is a core feature of borderline personality disorder (BPD). Previous studies have reported that abnormal grey matter volume is associated with the limbic–cortical circuit and default mode network (DMN) in patients with BPD. However, alterations of cortical thickness in adolescents with BPD have not been well evaluated. Objective: The aim of this study was to assess cortical thickness and its association with emotional dysregulation in adolescents with BPD. Method: This prospective study enrolled 52 adolescents with BPD and 39 age- and sex-matched healthy controls (HCs). Assessments included brain magnetic resonance imaging (MRI) acquisition with structural and resting-state functional MRI data, and clinical assessment for emotional dysregulation using the Difficulties in Emotion Regulation Scale (DERS). Cortical thickness and seed-based functional connectivity were analysed with FreeSurfer 7.2 software. Correlation analysis between cortical thickness and the scores from emotional assessment was performed with Spearman analysis. Results: Compared to HCs, there was altered cortical thickness in the DMN and limbic–cortical circuit in adolescents with BPD (Monte Carlo correction, all p < .05). These regions with altered cortical thickness were significantly associated with emotional dysregulation (all p < .05). There were also alterations of functional connectivity, i.e. with increased connectivity of the right prefrontal cortex with bilateral occipital lobes, or with the limbic system, and with decreased connectivity among the DMN regions (voxel p < .001, cluster p < .05, family-wise error corrected). Conclusions: Our results suggest that the altered cortical thickness and altered functional connectivity in the limbic–cortical circuit and DMN may be involved in emotional dysregulation in adolescents with BPD.