Objective To explore the clinical efficacy of repetitive transcranial magnetic stimulation （rTMS） on the children with Autism Spectrum Disorder （ASD） with varied stimulation parameters. Methods A total of 82 Han nationality Chinese children with ASD （according to DSM-5） who were divided into study group （n=41） and control group （n=41） by random were enrolled， with the average age （6.83±2.63） years. For the study group， the dorsolateral prefrontal cortex （DLPFC） of the participants were stimulated with high frequency on the left side， while with low frequency on the right side. For the control group， the bilateral DLPFC of the participants were stimulated with low frequency. All the participants were intervened for 8 weeks， 5 times per week. The childhood autism rating scale （CARS）， Repetitive Behavior Questionnaire-2 （RBQ-2）， Strengths and Difficulties Questionnaire （SDQ） & Short Sensory Profile （SSP） were used to assess the symptoms of ASD before the intervention， after session 1 and 2 respectively. Results A total of 79 participants completed the entire experiment. There was no statistical difference on the baseline data between the two groups. For the Repeated Measure ANOVA， in terms of CARS score， the difference of main effect between groups was not statistically significant ［F（1，76）=3.65， P=0.063）， the difference of main effect between treatment courses was statistically significant ［F（2，75）=82.154， P ＜ 0.01］； there was no significant interaction between group and course of treatment ［F（2，75）=0.153， P=0.696］. In terms of RBQ-2， the differences of the main effect between groups ［F（1，76）=5.273， P=0.012］， treatment courses ［F（2，75）=64.312， P ＜ 0.01］， and the interaction between group and treatment course ［F（2，75）=14.314， P=0.004］were all statistically significant. In terms of SDQ， the differences of the main effect between groups ［F（1，76）=7.321， P=0.011］， treatment courses ［F（2，75）=75.643， P＜ 0.01］， and the interaction between group and treatment course ［F（2，75）=8.752， P=0.005］were all statistically significant. In terms of SSP， the difference of main effect between groups was not significant ［F（1，76）=2.778， P=0.071］； the difference of main effect between treatment courses was statistically significant ［F（2，75）=122.306， P ＜ 0.01］； the interaction between groups and treatment courses was statistically significant ［F（2，75）=4.752， P=0.046］. Further analysis of the interaction between groups and treatment by simple effect analysis found that the scores of RBQ-2 in the study group were higher than those in the control group during session 1 （P=0.001） and session 2 （P=0.014）； the scores of SDQ in the study group were lower than those in the control group during session 1 （P=0.021） and session 2 （P=0.035）； the scores of SSP in the study group was higher than those in the control group during session 1 （P=0.027）. Conclusions Both high-frequency on left and low-frequency on right and bilateral low-frequency rTMS stimulation on DLPFC of children with ASD improve the symptoms. The treatment of high-frequency on left and low-frequency on right is helpful to control the emotion disorders， while bilateral low-frequency rTMS stimulation is helpful to control the repetitive stereotyped behavior and sensory abnormality.