Hypothalamus is a crucial deep brain area that is responsible for the integration and coordination of various brain functions. The altered perfusion of hypothalamus during headache caused by medication-overuse headache (MOH) was previously unknown. In the current study, the altered perfusion of hypothalamic subregions in MOH patients was investigated using state-of-the-art 3D pseudo-continuous arterial spin labeling (PCASL) MR imaging. In this study, 29 normal controls subjects (NCs) and 29 MOH patients underwent 3D PCASL and brain structural MR imaging. The hypothalamus was automatically segmented into 10 subunits and the volume of each subunit was automatically determined using Freesurfer software (v7.4.1). All segmented hypothalamic subunits were converted to individual hypothalamic subunit masks. The cerebral blood flow (CBF) images were coregistered with the raw brain structural images and resliced. The CBF value of each hypothalamic subunit was extracted from the warped CBF images. The volume and CBF value of each hypothalamic subunit were analyzed using the independent sample T test and Mann–Whitney U test, receiver operating characteristic (ROC) curve analysis, and Pearson and Spearman correlation analysis. Hypothalamic subunits with significantly decreased perfusion were located in the left posterior, left tubular superior, right anterior–inferior, right tubular inferior, right tubular superior, right posterior subunit and the entire right hypothalamus [CBF value for MOH vs NC (mL/100 g·min): 48.41 ± 6.75 vs 54.08 ± 11.47, 44.44 ± 4.79 vs 48.11 ± 7.73, 41.49 (32.90, 61.46) vs 49.38 ± 10.47, 46.62 ± 7.04 vs 53.90 ± 11.75, 42.12 ± 5.74 vs 47.02 ± 9.99, 42.79 ± 5.15 vs 47.93 ± 10.48 and 43.58 ± 5.06 vs 48.65 ± 9.33, respectively] in MOH compared to NC (
P
< 0.05). ROC analysis for these positive subunits revealed that area under the curve was 0.658–0.693, and ROC curve for left posterior subunit had the highest specificity of 93.10% while the entire right hypothalamus had the highest sensitivity of 72.41%. Further correlation analysis showed that the CBF value of the left posterior, right anterior–inferior, right tubular superior, whole right hypothalamus presented significantly negative correlation with Hamilton Depression Scale (HAMD) score (
P
< 0.05). Hypoperfusion of hypothalamic subunits may contribute to the understanding of MOH pathogenesis, and the 3D PCASL could be considered as a potential diagnostic and assessment tool for MOH.