Objective To study CT perfusion (CTP) and MR perfusion (PWI) weighted imaging in evaluating the effect of vascular reconstruction on short-term cerebral blood flow in patients with moyamoya disease. Methods 47 patients with unilateral vascular reconstruction confirmed by DSA in the hospital were selected as the research objects and all received vascular reconstruction. All the patients received CTP and PWI examination before and after operation to obtain parameters, such as cerebral blood volume (CBV), cerebral blood flow (CBF), mean transit time (MTT) and time to peak (TTP). The preoperative and postoperative distribution of cerebral middle artery (MCA) and ipsilateral cerebellar perfusion parameters in control part (rCBF, rCBV, rMTT and rTTP) were compared as well as the differences in preoperative and postoperative relative value of CTP and PWI perfusion parameters. Results Postoperative CT perfusion image showed that CBF, CBV, MTT and TTP in the right distribution area of MCA significantly changed, compared with those before operation. Postoperative PWI perfusion image showed that CBF, CBV, MTT and TTP significantly significantly changed, compared with those before operation. After operation, rCBF and rCBV values in the distribution area of operation side MCA and the control ares were significantly higher than those before operation (P<0.05) while rMTT and rTTP were significantly lower than those before operation (P<0.05). Conclusion Both of CT perfusion and MR perfusion weighted imaging are the effective observation methods to observe the changes of cerebral blood flow in patients with moyamoya disease, which can be used in clinic.