The nature of buffer system is a very important factor of determining the dynamic properties for the success of docking operation in space. The current buffer system is too large and highly complicated, which is not suitable for microspacecraft for On Orbit Servicing (OOS). In this paper, a new type of probe-cone docking mechanism with flexible docking cone as buffer system was presented, and the impact force was simulated using the explicit finite element code, LS-DYNA. Then, the time history of the impact process such as the velocity of docking probe and the docking cone’s displacement was computed under the given impact velocity and initial deviation. In the end, the influence of the wall thickness of docking cone on the impact force was analyzed. The conclusion that the flexible docking cone can greatly help to reduce the maximum impact force by more than 50% provides a basis for the engineering design of the buffer system.