Individual’s functional brain networks are sensitive indicators of behaviors. Atypical functional connectivity have been observed in children with autistic spectrum disorder (ASD), manifesting characteristic and distinctive behavior at ages of 2- to 7-years. However, little is known about individual variability of the functional brain networks in children with ASD. In this study, using resting-state fMRI and variability analysis, we quantified distinguished variability pattern in children with ASD from typically developing (TD) children from 2- to 7-years of age, especially in higher-order functional networks. The higher inter-subject variability in children with ASD may be associated with their impaired behaviors.