Objective Underconnectivity in the resting brain is not consistent in autism spectrum disorder (ASD). However, it is known that the functional connectivity of the default mode network is mainly decreased in childhood ASD. This study investigated the brain network topology as the changes in the connection strength and network efficiency in childhood ASD, including the early developmental stages. Methods In this study, 31 ASD children aged 2–11 years were compared with 31 age and sex-matched children showing typical development. We explored the functional connectivity based on graph filtration by assessing the single linkage distance and global and nodal efficiencies using resting-state functional magnetic resonance imaging. The relationship between functional connectivity and clinical scores was also analyzed. Results Underconnectivities within the posterior default mode network subregions and between the inferior parietal lobule and inferior frontal/superior temporal regions were observed in the ASD group. These areas significantly correlated with the clinical phenotypes. The global, local, and nodal network efficiencies were lower in children with ASD than in those with typical development. In the preschool- age children (2–6 years) with ASD, the anterior-posterior connectivity of the default mode network and cerebellar connectivity were reduced. Conclusion The observed topological reorganization, underconnectivity, and disrupted efficiency in the default mode network subregions and social function-related regions could be significant biomarkers of childhood ASD.