Objective To investigate the effects of medical service and education partnership intervention on rehabilitation of children with autism spectrum disorder (ASD) in special education. Methods Sixty-seven children with ASD were selected from special education schools. Gesell development scale for children aged 0 to 6 and community living scale were utilized by child health care physicians to evaluate the development level and community living level of children. Forty-eight children were classified into intervention group, individualized rehabilitation training targets were designed by physicians based on the evaluation results, and individualized rehabilitation training program was put forward and conducted by teachers in special education schools. The other 19 children were served as controls, and routine rehabilitation training of special education schools was carried out. After training for 12 months, all children were reevaluated by physicians with the same methods. Results Compared with the control group, children in the intervention group made more progress on adaptability, language and social life skills after training. The intervention effects of children of younger age (﹤ 7 years) were significantly better than those of older age (≥ 7 years) . Conclusion Medical service and education partnership intervention is beneficial to the promotion of development level and social life skills in children with ASD, and earlier intervention may be more effective.