<p>Childhood obstructive sleep apnea syndrome (OSAS) disrupts normal ventilation and sleep structure and affects cognitive functions. However, the neurophysiological mechanisms underlying cognitive impairment are unclear. This study investigates the topological connectivity of white matter networks in children with moderate to severe OSAS and explores the underlying mechanisms of cognitive impairment. We collected clinical data of patients with moderate to severe OSAS (<i>n</i> = 43) and non-OSAS (<i>n</i> = 30). Intelligence testing was conducted using the China Wechsler Intelligence Scale for Children-Fourth Edition (C-WISC IV), including Processing speed, Working memory, Verbal comprehension, Perceptual reasoning, and Full-scale intelligence quotient (FSIQ). DTI data were collected using 3.0T MRI scanner (Ingenia, Philips, Netherlands). White matter network topology connections were analyzed using FSL and DSI Studio and inter group differences were statistically assessed. The difference of clinical and intelligence test was calculated by two sample t-test. Pearson correlation analysis was employed to examine the correlation between the abnormal white matter network metrics and cognitive function in OSAS patients. Clustering coefficient (Cp) and global efficiency (Eg), nodal degree (Dc), and nodal efficiency (Ne) were lower in the OSAS group (<i>p</i> &lt; 0.05). Correlations between white matter network metrics and cognitive function: The Cp and Eg were positively correlated with Perceptual reasoning, and the shortest path length (Lp) was negatively correlated with Perceptual reasoning. The results indicate that there was impairment of cognitive function and abnormality of topological structural connectivity in white matter networks for children with OSAS. The Cp, Eg, and Lp correlate with Perceptual reasoning, indicating that abnormal topological structural connectivity of the white matter network might be neurofunctional basis for impaired perceptual reasoning.</p>