Objectives This study aims to explore the impact of a 12-week mini-basketball training program (MBTP) on social communication impairments and salience network in preschool children with autism spectrum disorder (ASD), and to reveal the potential neural mechanisms by which MBTP improves social communication impairments in ASD children. Methods 34 ASD children aged 3–6 were assigned to the experimental group (n = 19) or the control group (n = 15). The experimental group received MBTP for 12 wk, while the control group received routine behavioral rehabilitation interventions from institutions. Social communication impairments in preschool ASD children is measured with the Social Response Scale Second Edition (SRS-2). Functional connectivity of salience network before and after testing is evaluated by resting-state functional magnetic resonance imaging (rs-fMRI). Results This study suggests improvement in the social cognitive dimension of preschool ASD children with the aid of MBTP as well as optimization of the functional connectivity of ASD children’s salience network. The potential neural mechanism of MBTP in improving social cognitive dimension in ASD children involved changes in functional connectivity in the left middle frontal gyrus and left thalamus. Conclusions This study infers that the MBTP may not improve the social communication impairments of the ASD children while it is likely to improve social cognitive aspect of social communication impairments and reduce the maladaptive traits of ASD children. Under this circumstance, the study could provide new evidence to explore the neural mechanisms of physical exercise improving social communication impairments and new targets for developing exercise intervention programs to improve social communication impairments in ASD children.