||Background: Acupuncture has analgesic effect to most pain conditions. Many neuroimaging studies were conducted to explore acupoint specificity in pain and other condition, but till now there is still discrepancy. Based on our previous finding, this study investigated the brain metabolism changes of acupuncture analgesia induced by sub-specific acupoint and non-acupoint stimulation.Methods: 30 migraineurs were included and randomly assigned to 3 groups: Acupuncture Group (AG), Sham Acupuncture Group (SAG) and Migraine Group (MG). In AG, a combination sub-specific points of Shaoyang meridians, Luxi (TE19), San Yangluo (TE8), and Xi Yangguan (GB33) has been stimulated with electroacupuncture, while non-acupoints for SAG were used and MG received no treatment. Positron emission tomography with computed tomography (PET-CT) was used to identify differences in brain glucose metabolism between groups.Results: In the AG, brain glucose metabolism increase compared with the MG was observed in the middle frontal gyrus, postcentral gyrus, the precuneus, parahippocampus, cerebellum and middle cingulate cortex (MCC), and decrease were observed in the left hemisphere of Middle Temporal Cortex (MTC).In the SAG, compared with MG, glucose metabolism increased in the poster cingulate cortex (PCC), insula, inferior temporal gyrus, MTC, superior temporal gyrus, postcentral gyrus, fusiform, inferior parietal lobe, superior parietal lobe, supramarginal gyrus, middle occipital lobe, angular and precuneus; while, decreased in cerebellum, parahippocampus.Conclusions: Acupuncture stimulation at both sub-specific acupoint and non-acupoint yields ameliorating effect to migraine pain, but with evidently differed central mechanism as measured by PET-CT. The pattern of brain glucose metabolism change in acupoint is pertinent and targeted, while in non-acupoint that was disordered and randomized. These finding may provide new perspectives into the validation of acupoint specificity, optimizing acupuncture analgesia and revealing central mechanism of acupuncture analgesia by neuroimaging measurement.Trial Registration: This trial was registered in the Chinese Clinical Trial Registry, with registration no. ChiCTR-TRC-11001813.