Background: Distinguishing moyamoya disease (MMD) from intracranial atherosclerotic stenosis (IAS) is critical for its treatment and outcome evaluation. This study aimed to use the combined sequences of high-resolution magnetic resonance imaging (HRMRI) and arterial spin labeling MR (ASL-MR) to identify the two entities accurately. Methods: This prospective study enrolled 58 patients with middle cerebral artery (MCA) steno-occlusion identified by digital subtraction angiography (DSA), including 27 cases of MMD and 31 cases of IAS. All patients underwent MRA, HRMRI and ASL-MR prior to DSA. Two radiologists blinded to DSA results analyzed the MR images. The inner and outer diameters of the target arteries, the wall thickness of the stenotic segment, and the perfusion status in the territories of the target arteries [cerebral blood flow (CBF), cerebral blood volume (CBV) and arterial transit time (ATT)] were measured quantitatively. The differences between MMD and IAS regarding the aspects of HRMRI and Pseudo-continuous ASLMR (PCASL-MR) maps were analyzed based on both visual characteristics and data information. Results: Regarding the HRMRI images, ;FIND tended to have homogeneous and concentric vessel-wall thickening as well as collaterals adjacent to the stenotic vessels; while IAS showed eccentric and heterogeneous vessel-wall thickening. For the CBF maps of PCASL-MR, abnormal hyper-perfused spots embedded inside the hypo-perfused regions were observed in MMD instead of IAS. Quantitative analysis revealed that MNID displayed smaller inner and outer diameters, and smaller maximum wall thickness, higher average value of CBF, CBV and ATT, and higher maximum value of CBF and CBV, when compared to IAS (all P<0.01). The average wall thickness and the maximum value of ATT showed no significant difference between MMD and IAS (P>0.01). Conclusions: HRMRI combined with PCASL-MR may help distinguish MAID and IAS induced cerebral arterial stenosis and cerebral perfusion disorder accurately and non-invasively.