Right ventricular (RV) failure has become a deadly complication of left ventricular assist device (LVAD) implantation, for which desynchrony in bi-ventricular pulse resulting from a LVAD is among the important factor. This paper investigated how different control modes affect the synchronization of pulse between LV (left ventricular) and RV by numerical method. The numerical results showed that the systolic duration between LV and RV did not significantly differ at baseline (LVAD off and cannula clamped) (48.52% vs. 51.77%, respectively). The systolic period was significantly shorter than the RV systolic period in the continuous-flow mode (LV vs. RV: 24.38% vs. 49.16%) and the LV systolic period at baseline. The LV systolic duration was significantly shorter than the RV systolic duration in the pulse mode (LV vs. RV: 28.38% vs. 50.41%), but longer than the LV systolic duration in the continuous-flow mode. There was no significant difference between the LV and RV systolic periods in the counter-pulse mode (LV vs. RV: 43.13% vs. 49.23%). However, the LV systolic periods was shorter than the no-pump mode and much longer than the continuous-flow mode. Compared with continuous-flow and pulse mode, the reduction in rotational speed (RS) brought out by counter-pulse mode significantly corrected the duration of LV systolic phase. The shortened duration of systolic phase in the continuous-flow mode was corrected as re-synchronization in the counter-pulse mode between LV and RV. Hence, we postulated that the beneficial effects on RV function were due to re-synchronizing of RV and LV contraction. In conclusion, decreased RS delivered during the systolic phase using the counter-pulse mode holds promise for the clinical correction of desynchrony in bi-ventricular pulse resulting from a LVAD and confers a benefit on RV function.