In this research, a one-way coupling numerical method for the ship-helicopter dynamic interface was developed in combination with a Detached Eddy Simulation and a helicopter flight mechanics model. Using the method, the effects of the active and passive flow control (i.e., active jet and notch) on ship-helicopter dynamic interface was investigated, especially the control margin and unsteady aerodynamic loading characteristics of a shipborne helicopter. The results showed that although the notch modification could reduce the unsteady aerodynamic loading level, it also increased the lateral velocity component of the ship airwake, which led to the increase of the roll angle of the helicopter and the decrease of the pedal margin. In comparison, the active jet control could reduce pilot workload while had little adverse effect on control margin. The parametric studies indicated that the jet with proper strength and frequency can reduce the lateral turbulence intensity and turbulent kinetic energy levels, and alleviates the pilot workload, but if the strength and frequency is high, the small-scale vortex generated by the jet itself will make the ship airwake disordered, which has a negative effect on the control ability of the active jet to decrease the unsteady level of ship airwake. In addition, the control ability of the unsteady jet was not good as that of steady jet when the jet momentum coefficient was constant.