Impairments in social communication (SC) represent one of the core symptoms of autism spectrum disorder (ASD). While previous studies have demonstrated that exercise intervention improves SC in children with ASD, there is currently no neuroscientific evidence supporting its benefits. Therefore, we evaluated the outcomes of a long-term exercise intervention on SC and white matter integrity (WMI) in children with ASD, and further explored the neural mechanism of exercise intervention on SC in these children. Twenty-nine children aged 3–6 years with ASD were assigned to either exercise group (n = 15) or control group (n = 14). The exercise group received a scheduled mini-basketball training program (5 sessions per week, forty minutes per session) for 12 consecutive weeks, while the control group was instructed to maintain their daily activities. Groups were assessed before and after intervention on SC and WMI. SC scores were lower in the exercise group post-intervention. Compared with the control group, WMI of the exercise group showed higher fractional anisotropy in the body of corpus callosum, fornix, right cerebral peduncle, left posterior limb of internal capsule, right retrolenticular part of internal capsule, left anterior corona radiate and left superior fronto-occipital fasciculus; lower mean diffusivity in the left anterior corona radiate and the bilateral corticospinal tract. Furthermore, increased WMI was associated with lower scores on a measure of social cognition in the overall sample. This study is the first to provide evidence that exercise intervention improves SC and white matter integrity in children with autism.