Purpose Acupuncture has been recognized as an effective and safe alternative therapy for migraine, but its central mechanism has not yet been adequately explained. Meanwhile, research into the clinical efficacy and central mechanism of true acupuncture (TA) and sham acupuncture (SA) is lacking. It is necessary to investigate whether TA has better efficacy than SA, and how they achieve different effects. This study aims to evaluate the efficacy of TA and SA, observe the brain response caused by TA and SA, and further investigate the central nervous mechanism of TA and SA treatment for patients with migraine. Patients and Methods This is a randomized controlled neuroimaging trial combining acupuncture treatment with functional magnetic resonance imaging, with patients and outcome assessors blinded. A total of 60 patients with migraine will be randomly allocated to receive 12 sessions of either TA or SA treatments (three sessions per week for 4 weeks), and 30 healthy participants will be recruited as the healthy control (HC) group. Outcome assessment and neuroimaging will be conducted before and after the entire intervention. A headache diary and questionnaires of life quality and psychological properties will be used to evaluate clinical efficacy. Multimodal magnetic resonance imagining data analysis will be used to investigate the central mechanism of TA or SA in treating migraine. Pearson’s correlation analysis will be used to reveal the relationship between the brain response and clinical improvements. Conclusion The results of this study will reveal the brain response to TA and SA in patients with migraine and contribute to further expanding the knowledge of their central mechanism. Study Registration This trial has been approved by the ethics committee of Dongzhimen Hospital affiliated to Beijing University of Chinese Medicine (DZMEC-KY-2020-38) and registered in the Chinese Clinical Trial Registry (registration number ChiCTR2000033995).