Background <p>Studies have shown that patients with chronic migraine exhibit abnormalities in structural and functional brain networks. However, the underlying brain mechanisms that govern structural-to-functional connectivity coupling in this population remain unclear.</p> Methods <p>Multimodal functional MRI data were collected from 36 patients with chronic migraine without aura, 94 patients with episodic migraine without aura and 51 healthy controls. Spearman’s correlation analysis was used to calculate SC-FC coupling. The Kruskal–Wallis test was used to compare differences in SC-FC coupling between the three groups. We also performed a correlation analysis to investigate the associations between SC-FC coupling and clinical variables.</p> Results <p>Compared with the healthy control group, patients with episodic migraine exhibited abnormal SC-FC coupling in the right rolandic operculum, left lingual gyrus, left pallidum, and vermis 7. In contrast, patients with chronic migraine exhibited abnormal SC-FC coupling in the left cerebellum 3, vermis 7, and pulvinar nucleus of the thalamus. Patients with chronic migraine exhibited abnormal SC-FC coupling in the left pulvinar nucleus of the thalamus compared with patients with episodic migraine. SC-FC coupling in the left cerebellum 3 of patients with chronic migraine was significantly associated with disability scores (<i>r</i> = -0.3731, <i>p</i> = 0.0250).</p> Conclusion <p>Our study identified SC–FC coupling alterations associated with chronic migraine. This suggests that abnormalities in SC-FC coupling in subcortical nuclei and the cerebellum may represent underlying mechanisms of chronic migraine.</p>