To investigate the effective connectivity between the bilateral insulae and other regions of the whole brain in children with obstructive sleep apnea (OSA), and to reveal the relationships between these abnormal connections and cognitive dysfunction in this condition. Resting-state functional magnetic resonance imaging (rs-fMRI) data and clinical variables were collected from 55 children with OSA [5.0 (5.0, 8.0) years, 32 males, 28 pre-school children] and 25 healthy controls [6.0 (5.0, 9.0) years, 11 males, 9 pre-school children], matched for age, gender, and education. Rs-fMRI data were analysed to investigative group-difference in the effective connectivity between the bilateral insulae and other regions of the brain of children with OSA with those of controls. Spearman correlation analysis was conducted between these abnormal connections and clinical variables among children with OSA. Compared with controls, children with OSA showed abnormal clinical variables (i.e., increased OAHI, AHI, OAI, HI, ODI, time of SpO