Background: To study the impact of acupuncture treatment on structural brain network for patients with different courses of migraine without aura based on fMRI. Methods: A total of ten patients with a long course (>5 years) of migraine without aura (MWoA), ten patients with a short course (<5 years) of MWoA, and ten healthy volunteers were recruited in this trail. All patients received acupuncture treatment three times per week for four weeks. The changes in the topology properties of structural brain regions were observed via fMRI. The clinical symptom scores were adopted for evaluating the therapeutic effect. Results: 1) The small-world property on the group with a long course was decreased significantly (p<0.01) after treatment, while the group with a short course increased (p<0.01). 2) The clustering coefficient or nodal local efficiency of brain nodes (including the pontine crossing tract, left corticospinal tract, right medial lemniscus, left posterior limb of the internal capsule, right cingulum hippocampus, left fornix, left superior longitudinal fasciculus and right tapetum) showed significant changes (p<0.001) with an opposite tendency on the two groups after treatment. 3) The left posterior limb of the internal capsule (p<0.001, R=-0.73) and right tapetum (p<0.05, R=-0.54) had a strong relationship with migraine courses. Conclusions: The two unequal ways of acupuncture on the structural brain network of migraineurs with different disease courses were revealed. Acupuncture could regulate the central sensitization of chronic migraines, differently with the early stage. The nodal efficiency of the left posterior limb of the internal capsule and right tapetum would be symbols to discriminate against the process of MWoA.