In the one-gravity environment on the ground, the simulation of the contact process of two flying objects in the zero-gravity environment of space has been a challenging issue since humans first explored space by flying objects. Hardware-in-the-loop(HIL) simulation is an important and effective method to test the usability, reliability, and safety of real docking mechanisms in space. There are four main issues for HIL simulation systems: Design of simulators capable of high frequency response, high motion precision, high velocity, and rapid acceleration; compensation for simulation distortion; design of a control model for the HIL simulation process; and experimental verification. Here, we propose a novel HIL simulator system with a 6-DOF 3-3 perpendicular parallel mechanism and a 3-DOF 3-PRS parallel mechanism; discover the principle of simulation distortion; present distortion compensation models for the force measurement system, dynamic response, and structural dynamics of the simulator; and provide a control model for the HIL simulation process. Two kinds of experiments were performed on the passive-undamped elastic rod and the docking mechanisms to test their performances and to verify the effectiveness and usability of the HIL simulator. The HIL simulation system proposed in this paper is useful for developing space docking, berthing, refueling, repairing, upgrading, transporting, and rescuing technologies. In the one-gravity environment on the ground, the simulation of the contact process of two flying objects in the zero-gravity environment of space has been a challenging issue since humans first explored space by flying objects. Hardware-in-the-loop ( There are four main issues for HIL simulation systems: Design of simulators capable of high frequency response, high motion precision, high velocity , and rapid acceleration; compensation for simulation distortion; design of a control model for the HIL simulation process; and experimental verification. Here, we propose a novel HIL simulator system with a 6-DOF 3-3 perpendicular parallel mechanism and a 3-DOF 3-PRS parallel mechanism; discover the principle of modeling distortion; present distortion compensation models for the force measurement system, dynamic response, and structural dynamics of the simul ator; and provide a control model for the HIL simulation process. Two kinds of experiments were performed on the passive-undamped elastic rod and the docking mechanisms to test their performances and to verify the effectiveness and usability of the HIL simulator. The HIL simulation system proposed in this paper is useful for developing space docking, berthing, refueling, repairing, upgrading, transporting, and rescuing technologies.