Objective To investigate the hemodynamic effects of enhanced external counterpulsation (EECP) on cerebral arteries with different stenoses. Methods Zero-dimensional/three-dimensional multiscale hemodynamic models of cerebral arteries with different stenoses were constructed. Numerical simulations of the EECP hemodynamics were performed under different counterpulsation modes to quantify several hemodynamic indicators of the cerebral arteries. Among them, the mean time-averaged wall shear stress (TAWSS) downstream of the stenosis was in the range of 4–7 Pa, a low percentage of risk TAWSS area, and high narrow branch flow were considered to inhibit the development of atherosclerosis and create a good hemodynamic environment. Results For cerebral arteries with 50%, 60%, 70%, and 80% stenosis, the hemodynamic environment was optimal in counterpulsation mode when the moment of cuff deflation was 0.5, 0.6, 0.7, and 0.7 s within the cardiac cycle. Conclusions For 50% stenotic cerebral arteries, the counterpulsation mode with a deflation moment of 0.5 s should be selected. For 60% stenotic cerebral arteries, the counterpulsation mode with a deflation moment of 0.6 s should be selected. For 70 or 80% stenotic cerebral arteries, the counterpulsation mode with a deflation moment of 0.7 s should be selected. As stenosis of the cerebral arteries increases, the pressure duration should be prolonged. This study provides a theoretical reference for the EECP treatment strategy for patients with ischemic stroke with different stenoses.