Objective: The comorbidity of migraine and depressive has been recognized, but the pathophysiology remains unknown. Here, we aimed to explore the structural change of amygdala(AMY) and abnormal function in the centromedial amygdala (CMA) among migraineurs with depression. Methods: High-resolution T1-weighted and functional magnetic resonance images were acquired from subjects of 22 migraine comorbid with depression(EMwD ), 22 episodic migraine (EM), 20 major depressive disorder (MDD), respectively, and 18 healthy controls(HC). Apply voxel-based morphometry (VBM ) and resting state functional connectivity (rsFC) to examing inter-group differences in brain structure and function. Results: The volume of bilateral AMY increased in EMwD and EM compared to HC. EMwD showed larger volume than MDD. And the volume of AMY showed positive correlation with duration of illness in patient groups. Compared with EM, EMwD exhibited decreased rsFC between the right CMA and left cerebellum, left dorsolateral prefrontal cortex (DLPFC) , left precuneus(PCC). In addition, rsFC between the left CMA and left DLPFC was negatively correlated with Hamilton Anxiety Scale (HAMA), Hamilton Depression Scale (HAMD). Conclusions: According to our findings, the larger volume of amygdala and the abnormal functional connectivity may help to determining the common symptoms in migraine with depression, and may be a treatment target for migraine and depression comorbidities.