Continuous blood pressure is measured from various extracranial body sites, with difference in amplitude and phase with intracranial blood pressure. Consequent influences on the accuracy of Windkessel model need further investigation. Between blood pressure and intracranial flow rate, a model with non-linear flow resistance (R-DT) was proposed and compared with the 3-element Windkessel (RCR) model. From the measured blood flow velocity in middle cerebral artery, the blood pressure was estimated by R-DT and RCR models respectively. The parameters in the models were optimized by genetic algorithm. The accuracies of R-DT and RCR models were compared based on their estimation errors to the measured blood pressure. The capacitance element in RCR model indicated limited ability to take the time shift into account. Compared with RCR model, R-DT model had less error (averaged relative error: 5.19% and 2.49% for RCR and RDT models). The non-linear flow resistance was applicable in simulating cerebral arteries.