Intra-aorta pump is a novel rotary ventricular assist device. Because of the special structure and connection with the native heart, the hemodynamic effect of support mode of this pump on the cardiovascular system is not clear. In this work, three support modes, including “constant speed” mode, “co-pulse” mode, and “counter-pulse” mode, have been designed for the intra-aorta pump to evaluate the hemodynamic effect of different support modes on the cardiovascular system. Simulation results demonstrate that that both “co-pulse” mode and “counter-pulse” mode can achieve better unloading performance than “constant speed” mode. The intra-aorta pump controlled by “co-pulse” mode is beneficial for improving coronary flow. Moreover, the external work, which is defined as the product of left ventricular pressure and cardiac output, under “co-pulse” mode is the minimum of the three support modes (0.783 w vs. 0.615 w vs. 0.702 w). The pulsatility ratio, defined as the ratio of the peak-to-peak value of arterial pressure (AP) to the mean arterial pressure value, under “co-pulse” mode is the maximum of the three modes (24% vs. 32.8% vs. 23.7%). The equivalent afterload value, which is the ratio of pulsatile pressure at the pump inflow and pulsatile pump flow, is larger than other support modes (0.596 mm Hg.s/mL vs. 0.9704 mm Hg.s/mL vs. 0.55 mm Hg.s/mL). In brief, the intra-aorta pump under “co-pulse” mode support is beneficial for improving myocardial perfusion and restoring pulsatility of AP, while “counter-pulse” mode is beneficial to the perfusion of vital organs.