In order to enable continuous-flow left ventricular assist device (CFLVAD) to adjust pump speed adaptively in response to changes in ventricular load, we developed a multi-objective physiological control system for CFLVAD with non-invasive physiological feedback mechanism, and proposed a multi-objective hierarchical control (MOHC) strategy to coordinate three controllers. A model-based estimation method was utilized to gain the physiological feedback variables. Suction prevention controller, regurgitation prevention controller, and physiological pulsatility controller were developed and applied to achieve the objectives: preventing left ventricular suction, preventing pump regurgitation, pump flow adaptive adjustment, and enhancing vascular pulsatility. The constraint conditions of feedback variables and controller priority were used to implement multi-objective hierarchical control. The preload and afterload were increased or decreased to simulate the scenarios of the sharp increase in left ventricular flow, the sharp decrease in left ventricular flow, and the rest-exercise-rest. The performance of MOHC was evaluated by subjecting it to three scenarios and compared with that of constant speed control (CSC) and pulsatile varying speed control (PVSC). The simulation results show that the linear correlation between the filtered and actual feedback variables was as high as 99.9%. Compared with CSC and PVSC, MOHC can avoid ventricular suction and pump regurgitation when the left ventricular flow changed rapidly. During rest or exercise, MOHC provided more adequate physiological perfusion and enhances greater vascular pulsatility than CSC and PVSC. MOHC can adjust the CFLVAD pump speed in response to changes in ventricular load.