Numerous studies demonstrated that the locus coeruleus (LC)was activated by acute nociceptive pain and played important role during the maintenance of chronic pain. The purpose of the study was to assess the morphology and cerebral blood flow (CBF) changes of LC in chronic migraine(CM) patients and to explore their correlation with CM clinical features using three-dimensional pseudo-continuous arterial spin labeling(3D PCASL), aiming to provide a better understanding of LC role in CM pathophysiology. Thirteen patients diagnosed of CM at Department of Neurology, Hainan Hospital of Chinese PLA General Hospital from May 2020 to June 2021 were prospectively included and fifteen age and sex-matched normal controls (NCs) were enrolled. All the participants received psycho-neurological assessment and undertook brain structural and 3D PCASL MRI examination. Volume and CBF alterations were assessed, correlation analysis with clinical scores were undertaken, and the receiver operating characteristic (ROC) curves analysis were conducted between groups. No statistical differences were found in the total volumes of LC between CM patients and NCs (P > 0.05). Compared with the NCs, the CBF in bilateral LC were lower in the CM patients, and the decrease in the right side has significant statistical value(P = 0.031). Correlation analysis revealed a negative association between the CBF of LC with duration of the disease (years). ROC curves analysis showed that the curve area for the CBF of the right LC was 0.749(95% CI 0.563–0.935), and the optimal cut-off point of value, sensitivity, and specificity for distinguishing CM from NC was 49.67 ml/100mg.min, 0.53 and 0.92, respectively. Hypoperfusion of bilateral LC was observed in CM. The altered CBF value of LC was negatively correlated with the disease duration. LC perfusion may hold promise as a potential early diagnostic imaging biomarker for CM.