Purpose: We investigated the relationship between hemodynamic sources of recipient arteries and the microvascular transit time (MVTT) to explain the underlying mechanisms of cerebral hyperperfusion syndrome (CHS) in individuals with moyamoya disease (MMD). Methods: Forty-two adult individuals with MMD that underwent superficial temporal artery–middle cerebral artery (STA-MCA) bypass surgery between July 2020 and January 2021 were included in the analysis. Enrolled individuals underwent digital subtraction angiography (DSA) to diagnose MMD and determine the hemodynamic sources of recipient arteries (MCA or non-MCA), as well as intraoperative indocyanine green video angiography to measure MVTTs. Correlations between the hemodynamic sources of recipient arteries and the MVTT were analyzed. Results: Seventeen surgical hemispheres (40.5%) displayed a MCA-derived recipient artery and 25 hemispheres (59.5%) a non-MCA-derived recipient artery. Preoperative MVTT and DMVTT (the difference between preoperative and postoperative MVTTs) were significantly prolonged in the MCA-derived group (4.00±1.4 s and 1.96±1.48 s) compared to the non-MCA-derived group (2.79±0.79 s and 1.55±0.86 s). The incidence of CHS was 9.5% (4/42), with 3 CHS cases in the MCA-derived group and 1 CHS case in the non-MCA-derived group. Multivariate linear regression showed that hemodynamic sources of recipient arteries were related to preoperative MVTT (P = 0.004) and DMVTT (P < 0.001). Conclusions: The MVTTs of recipient vessels in the MCA-derived group were in general longer than those in the non-MCA-derived group. This may be due to abnormal hemodynamics. As well, this could account for the higher incidence of CHS in MMD patients with MCA-derived recipient vessels compared to non-MCA-derived vessels after STA-MCA bypass surgery.