Exercise intervention has been proven helpful to ameliorate core symptoms of Autism Spectrum Disorder (ASD). However, the underlying mechanisms are not fully understood. In this study, we carried out a 12-week mini-basketball training program (MBTP) on ASD children and examined the changes of brain functional and structural networks before and after exercise intervention. We applied individual-based method to construct functional network and structural morphological network, and investigated their alterations following MBTP as well as their associations with the change in core symptom. Structural MRI and resting-state functional MRI data were obtained from 58 ASD children aged 3-12 years (experiment group: n = 32, control group: n = 26). ASD children who received MBTP intervention showed several distinguishable alternations compared to the control without special intervention. These included decreased functional connectivity within the sensorimotor network (SM) and between SM and the salience network, decreased morphological connectivity strength in a cortical-cortical network centered on the left inferior temporal gyrus, and a subcortical--cortical network centered on the left caudate. Particularly, the aforementioned functional and structural changes induced by MBTP were associated with core symptoms of ASD. Our findings suggested that MBTP intervention could be an effective approach to improve core symptoms in ASD children, decrease connectivity in both structure and function networks, and may drive the brain change towards normal-like neuroanatomy.