Numerous studies have demonstrated that the locus coeruleus (LC) is activated by acute, nociceptive pain and plays an important role in the management of chronic pain. The purpose of this study was to assess the morphology and cerebral blood flow (CBF) changes in the LC of chronic migraine (CM) patients and explore the associations between these changes and the clinical features of these patients via three-dimensional pseudocontinuous arterial spin labelling (3D PCASL) in order to better elucidate the role of the LC in the pathophysiology of CM. Thirteen patients diagnosed with CM at the Department of Neurology, Hainan Hospital of PLA General Hospital, from May 2020 to June 2021 were prospectively included, and fifteen age- and sex-matched normal controls (NCs) were enrolled. All participants underwent psychoneurological assessments and brain structural and 3D PCASL MRI examinations. Brain region volume and CBF alterations were assessed, their associations with clinical scores were analysed, and receiver operating characteristic (ROC) curve analysis was conducted to determine the variables that best differentiated between the groups. No significant differences were found in the total volume of the LC between CM patients and NCs (P > 0.05). Compared with that in the NCs, the CBF of the bilateral LCs was lower in CM patients; the difference on the right side was statistically significant (P = 0.031). Correlation analysis revealed a negative correlation between the CBF of the LC and disease duration (in years). ROC curve analysis revealed that the area under the curve of the CBF of the right LC was 0.749 (95% CI 0.563-0.935), and the optimal cut-off value, sensitivity, and specificity in distinguishing CM patients from NCs were 49.67 ml/100 mg/min, 0.53 and 0.92, respectively. Hypoperfusion of the bilateral LC was observed in CM patients and contributes to the understanding of the pathogenesis of CM. 3D PCASL could serve as a useful tool for diagnosing and assessing CM.