Objective To explore the application effect of sensory integration training combined with repetitive transcranial magnetic stimulation (rTMS) therapy in children with autism spectrum disorder (ASD), providing a reference for the development of treatment programs for children with ASD. Methods A total of 98 children with ASD admitted to Luoyang Maternal and Child Health Hospital from June 2021 to June 2023 were selected for the study, and were randomly divided into a control group and an observation group (n=49). The control group were treated with sensory integration training, and 49 cases in the observation group were treated with rTMS combined with sensory integration training. The clinical efficacy, scores of the Psychoeducational Profile (PEP) for children with autism, scores of the Autism Behavior Checklist (ABC) , and Autism Treatment Evaluation Checklist (ATEC) scores were compared between the two groups of children. The value of multimodal parameters such as scores of the PEP, ABC and ATEC in predicting the effectiveness of treatment was analyzed. Results After treatment, the total effective rate of the observation group was higher (P<0.05). After the treatment, the scores of the PEP in both groups increased (P<0.05), and the score in the observation group was higher (P<0.05). After the treatment, the scores of the ABC in both groups decreased (P<0.05), and the score in the observation group was even lower (P<0.05). After the treatment, the scores of the ATEC in both groups decreased (P <0.05), and the score in the observation group was even lower (P <0.05). Receiver operating characteristic (ROC) curve analysis showed that the optimal cut-off points for the multimodal parameters of the PEP, the ABC, and ATEC in predicting the value of treatment effectiveness were 124 points, 66 points, and 51 points, respectively, the sensitivity, specificity and area under the curve (AUC) of the combined prediction were 85.71%, 98.68% and 0.918, respectively. Conclusion Sensory integration training combined with rTMS has a definite therapeutic effect on children with ASD and can improve their psychological state and autism symptoms. The combined prediction of multimodal parameters for the therapeutic effect of children with ASD is of higher value.