Executive function (EF) deficits are widely documented in children with developmental coordination disorder (DCD), yet little is known about their emergence during the preschool years and their underlying neural mechanisms. This study investigated EF performance and cortical development in 125 children aged 3-6 years, including those with and without DCD. Behavioral tasks assessed inhibitory control, cognitive flexibility, and working memory, while structural MRI was used to evaluate cortical thickness across five large-scale brain networks: frontoparietal, dorsal attention, ventral attention, default mode, and limbic networks. Results showed that children with DCD performed significantly worse on all EF tasks compared to typically developing peers. Across the full sample, EF performance was negatively correlated with cortical thickness, consistent with typical developmental patterns of synaptic pruning and neural efficiency. However, this relationship was absent in the DCD group, suggesting atypical structure-function coupling. These findings highlight that EF deficits are already present in preschool-aged children with DCD and that atypical neural pathways may underlie their early cognitive difficulties. From an applied perspective, identifying such early biomarkers offers critical insights for timely interventions, emphasizing the importance of integrating neuroscientific evidence into educational and clinical practices to support children at risk.