To improve the take-off and landing safety of shipborne helicopters, a numerical method based on one-way coupling strategy was developed for the study of ship-helicopter dynamic interface, with which the effect of different active flow control configurations on helicopter shipboard landing was analyzed under crosswind condition. First, the ship airwake data under different jet control conditions was obtained by using detached eddy simulation (DES). Then, the unsteady airloads and control margins during the shipboard landing were obtained by coupling the ship airwake data with the flight dynamics model. The effect of the active flow control at different locations on ship-helicopter dynamic interface under crosswind condition was investigated, in terms of unsteady loading levels and control characteristics of shipborne helicopter. Results show that the two active jet control configurations could both reduce the unsteady loading levels during the lateral translation of the helicopter. For the configuration that the jet outlet located at hangar vertical edge, the decoupling of unsteady characteristics and spatial characteristics could be realized, and the helicopter control margin was not reduced. While the configuration that the jet outlet located at the horizontal edge could increase the lateral velocity component of ship airwake and reduce the pedal margin. In addition, with the jet velocity increased, the control ability of jet decreased under the first configuration, and it increased first and then decreased under the second configuration.