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To summarize the clinical neuroimaging evidence pertaining to the potential mechanisms of acupuncture for migraine prophylaxis. From a descriptive perspective, converging evidence from recent neuroimaging studies, mainly from functional MRI (fMRI) studies, has demonstrated that when compared with sham acupuncture, verum acupuncture could normalize the decrease of the functional connectivity of the rostral ventromedial medulla-trigeminocervical complex (RVM/TCC) network, frontal-parietal network, cingulo-opercular networks, and default mode network and could normalize sensorimotor network connectivity with sensory-, affective-, and cognitive-related brain areas. These areas overlap with those of the pain matrix. Verum acupuncture works in a more targeted and unique manner compared with sham acupuncture in patients with migraine. These findings from neuroimaging studies may provide new perspectives on the validation of acupoints specificity and confirm the central modulating effects of acupuncture as a migraine prevention treatment. However, the exact mechanism by which acupuncture works for migraine prophylaxis remains unclear and warrants investigation. Future studies with larger sample sizes are still needed to confirm the current results and to further evaluate the complex and specific effects of acupuncture by analyzing different stimulus conditions, such as verum vs. sham acupuncture, deqi vs. no deqi, different acupuncture points or meridians, and different manipulation methods. Moreover, instead of focusing on the changes in a single area of the brain, researchers should focus more on the relationships among the functional connectivity network of brain areas such as the RVM/TCC, thalamus, anterior cingulate cortex (ACC), superior temporal gyrus (STG), and supplementary motor area (SMA) to explore the underlying mechanism of the effects of acupuncture.