Objective: To explore the dynamic features of intrinsic brain activity measured by fMRI in children with benign epilepsy with centrotemporal spikes (BECTS) and examine whether these indexes were associated with behaviors.Methods: We recruited 26 children with BECTS (10.35 ± 2.91 years) and 26 sex-, and age-matched (11.35 ± 2.51 years) healthy controls (HC) and acquired resting-state functional magnetic resonance imaging (rs-fMRI) and behavioral data. Dynamic regional homogeneity (dReHo), including mean and coefficient of variation (CV) metrics derived from the rs-fMRI data, and were compared between the BECTS and the HC groups.Results: Significantly decreased mean dReHo in bilateral supramarginal gyrus, left middle temporal gyrus (MTG.L), left postcentral gyrus and superior occipital gyrus were found in children with BECTS. Meanwhile, increased CV of dReHo in MTG.L and right fusiform in children with BECTS was revealed compared with HC. Further analyses of functional connectivity revealed decreased global signal FC existed in similar regions, linked with linguistic, social cognition, and sensorimotor processes, in children with BECTS compared with HCs. Moreover, the association analyses showed that the CV of dReHo in MTG.L was positively associated with age and a negative correlation was found between mean dReHo of MTG.L and disease duration. Besides, the CV of dReHo in MTG.L was found positively associated with the intelligence quotient (IQ) language scores and full IQ scores in children with BECTS, and the CV of dReHo in the left inferior temporal gyrus and Rolandic operculum were positively correlated with IQ operation scores and full IQ scores.Conclusion: Aberrant dynamic regional coherence in sensorimotor, linguistic, and lateral temporal regions suggests dynamical interplay that underlying cognitive performance in children with BECTS, suggesting an intrinsic dynamic mechanism for BECTS.