Introduction: Moyamoya disease (MMD) is a vascular disease with significant risk of mortality due to ischemia or hemorrhage in the brain. The goal of the study was to explore three-dimensional arterial spin labeling (3D-ASL) to improve evaluation of cerebral hemodynamics in patients with MMD. Methods: Our study included 54 cases of ischemic MMD and 42 cases of hemorrhagic MMD. Dynamic susceptibility contrast-enhanced perfusion-weighted imaging (DSC-PWI) and 3D-ASL were performed at 3.0 T. Based on these scans, cerebral blood flow (CBF), mean transit time (MTT), and time to peak (TTP) were calculated and compared between patients with different disease subtypes. Receiver operating characteristics analysis was used to assess the diagnostic sensitivity and specificity of different imaging procedures and parameters. Results: Our data suggested that CBF in the lesion area was more severely reduced in patients with hemorrhagic MMD than in those with ischemic MMD. The CBF parameter in 3D-ASL diagnosed hemorrhagic and ischemic MMD with a significant sensitivity and specificity of 80.59% and 57.41%, respectively, with an area under the curve (AUC) of 0.75. We also found that the relative CBF of 3D-ASL was more pronounced decreased and the relative MTT and TTP of DSC-PWI were significantly increased in patients with hemorrhagic MMD than those with ischemic MMD. Specificity and sensitivity and AUC of 3D-ASL were better than the comparison of absolute values from DSC-PWI scans. Conclusion: Our study indicated that 3D-ASL is powerful in differentiating patients with cerebral ischemic or hemorrhagic MMD, providing another diagnostic tool that could potentially improve precision medicine to monitoring MMD patients.