Generalized tonic-clonic seizure (GTCS) is a condition that is characterized by generalized spike-wave discharge in bilateral cerebral hemispheres during the seizure. Although previous neuroimaging studies revealed functional abnormalities in the brain activities of children with GTCS, the topological alterations in whole-brain networks remain poorly understood. The present study used graph theory to investigate the topological organization of functional networks in 13 GTCS children and 30 age-matched healthy controls. We found that both groups exhibited a small-world topology of the functional network. However, children with GTCS showed a significant decrease in nodal local efficiency and clustering coefficient in some key nodes compared with the controls. The connections within the default mode network (DMN) were decreased significantly, and the internetwork connections were increased significantly. The altered topological properties may be an effect of chronic epilepsy. As a result, the optimal topological organization of the functional network was disrupted in the patient group. Notably, clustering coefficient and nodal local efficiency in the bilateral temporal pole of the middle temporal gyrus negatively correlated with the epilepsy duration. These results suggest that the bilateral temporal pole plays an important role in reflecting the effect of chronic epilepsy on the topological properties in GTCS children. The present study demonstrated a disrupted topological organization in children with GTCS. These findings provide new insight into our understanding of this disorder. © 2020 The Authors. Brain and Behavior published by Wiley Periodicals LLC.