A docking mechanism and its control scheme ate discussed for high performance autonomous docking systems. A discussed problem is to achieve soft docking and to absorb the shock of collision when a satellite approaches to the docking mechanism with relative velocity. To solve the problem an intelligent adaptive structure is examined to use as the docking mechanism. Control strategy for the docking mechanism is discussed and a PD-impedance control, i.e., impedance control combined with PD-control, is proposed. The docking mechanism is controlled along an appropriate trajectory by using the PD-impedance control and the soft docking is achieved. Advantage of the PD-impedance control is discussed through a simple example. Finally, feasibility of the proposed scheme is verified by numerical simulations.