The impact of chronic cerebral hypoperfusion on resting-state blood oxygen level-dependent signal fluctuations remains unknown. We aimed to determine whether chronic ischemia induces changes in amplitude of low-frequency fluctuations (ALFF) and to investigate the correlation between ALFF and perfusion-weighted magnetic resonance imaging (PWI) parameters in patients with moyamoya disease (MMD). Thirty patients with pre- and postoperative resting-state functional magnetic resonance imaging and PWI were included, and thirty normal controls underwent resting-state functional magnetic resonance imaging. A decrease in preoperative frontal lobe ALFF was observed in patients with MMD. Postoperative frontal lobe ALFF showed moderate improvement but still remained lower than those in normal controls. The values of mean transit time and time-to-peak, but not cerebral blood volume and cerebral blood flow, correlated significantly with frontal lobe ALFF. Moreover, there were significant negative correlations between changes in frontal lobe PWI parameters and changes in frontal lobe ALFF on both operated side and contralateral side after the unilateral revascularization surgery. Our results demonstrate that reduced ALFF are closely related to the abnormal PWI parameters and vary with the alteration of cerebral perfusion in patients with MMD.