Brain networks provided powerful tools for the analysis and diagnosis of epilepsy. This paper performed a pairwise comparative analysis on the brain networks of Benign Childhood Epilepsy with Centrotemporal Spikes (BECTS): spike group (spike), non‐spike group (non‐spike), and control group (control). In this study, fragments with and without interictal spikes in electroencephalograms of 13 BECTS children during non‐rapid eye movement sleep stage I (NREMI) were selected to construct dynamic brain function networks to explore the functional connectivity (FC). Graph theory and statistical analysis were exploited to investigate changes in FC across different brain regions in different frequency bands. From this study, we can draw the following conclusions: (1) Both spike and non‐spike have lower energy in each brain region on the γ band. (2) With the increase of the frequency band, the FC strength of spike, non‐spike and control groups are all weakened. (3) Spikes are correlated with brain network efficiency and the small‐world property. (4) Spikes increase the FC of temporal, parietal and occipital regions except in the γ band and the absence of spikes weakens the FC of the entire brain region.