Background. As a central nervous system disease, migraine often coexists with gastrointestinal disorders, which suggests a disruption of brain-gut regulation. Clinical studies have confirmed that acupuncture and flunarizine not only alleviate migraine attacks but also substantially inhibit accompanying gastrointestinal symptoms. However, it is still not clear how acupuncture and flunarizine regulate the interactions of brain, gut, and microbiome. Therefore, this study will combine neuroimaging technology and gut microbiota detection technology to explore and compare the effects and brain-gut modulating mechanisms of acupuncture and flunarizine for migraine. Methods. This randomized clinical trial will recruit 66 patients with migraine without aura. Participants will be randomly assigned in a 1 : 1 ratio to an acupuncture group or a control group. The acupuncture treatment strategy is based on experience from our previous study and consensus meetings with clinical experts. Patients will receive 12 sessions of manual acupuncture treatment (once every other day to a total of three times per week, followed by a 2-day break). Flunarizine will be administered at a dose of 5 mg daily in the control group. Participants in both groups will receive treatment for a period of 4 weeks. The primary outcome is the change in frequency of migraine attacks, and the secondary outcomes include the changes in migraine days (days on which migraine attacks occurred), average migraine severity, gastrointestinal symptoms, psychiatric symptoms, and quality of life. Fresh stool samples will be collected, and 16S ribosomal RNA gene sequencing analysis will be used for gut microbiota. Magnetic resonance imaging will be applied to detect between-group changes in brain function. The abovementioned indicators will be collected at baseline, after a 4-week intervention, and at the 12-week follow-up. Discussions. From the perspective of brain-gut regulatory mechanisms, we will combine brain neuroimaging and gut microbiological data to partially reveal the similarities and differences of acupuncture and flunarizine on the treatment of migraine. The trial is registered with ChiCTR2000034417.