Abstract: Objective To explore the effect of comprehensive rehabilitation intervention with deep repetitive transcranial magnetic stimulation (rTMS) among autism spectrum disorder (ASD) children. Method Controlled clinical trial was used. A total of 20 3-6 years old ASD children who treated by rTMS and structured teaching (TEACCH) were selected as the intervention group. And, 20 ASD children whose sex and age-matched with intervention group and treated only by TEACCH were recruited as the control group. All of those children were recovering 6 months The curative effect of the control group and intervention group was compared. Result After intervention, there were significant difference in total scale and subscales score between the intervention group and the control group (P< 0.05). Before and after intervention, the difference of ATEC scale total score was statistically significant (P< 0.05) between the two groups.Conclusion There are significantly improvements of the main clinical manifestations among ASD children through the training by rTMS combined with TEACCH or TEACCH. The rehabilitation effect of rTMS combined with TEACCH is much better.