To evaluate the clinical value of NeuroGam software in assessing the brain foci perfusion changes by TC-ECD single photon emission computed tomography/computed tomography (SPECT/CT) brain imaging in patients with Moyamoya Disease (MMD).Seventy-two patients with MMD who underwent superficial temporal artery-middle cerebral artery (STA-MCA) bypass combined with encephalo-duro-myo-synangiosis (EDMS) surgical revascularization were included. Baseline and follow-up TC-ECD SPECT/CT brain scans were performed on all patients at least twice before and after operation. Pre- and post-SPECT dicom images were reoriented into Talairach space using NeuroGam Software package. Additional visual analysis was performed. Differences mean pixel value between pre- and post- operation brain perfusion were assessed with paired t test and McNemar test.Significant differences in the number of hypoperfusion foci were found between visual assessment and NeuroGam aided assessment. More hypoperfusion foci were found by NeuroGam software aided assessment in the frontal, parietal, temporal, occipital lobe, thalamus, basal ganglia and cerebellum before and after surgery (P < .0001). According to NeuroGam software assessment, the perfusion of frontal, parietal, temporal lobe, anterior and middle cerebral regions on the operative side significantly improved before and after surgery (t = -3.734, t = -3.935, t = -5.099, t = -4.006, t = -5.170, all P < .001). However, no significant differences were found in the occipital lobe (t = -1.962, P = .054), thalamus (t = 1.362, P = .177), basal ganglia (t = -2.394, P = .019), and cerebellum (t = 1.383, P = .171) before and after surgery.The NeuroGam software provides a quantitative approach for monitoring surgical effect of MMD in a variable time (3-12 months after surgery). It could discover the perfusion changes that are neglected in conventional visual assessment.