Simulation systems with hardware-in-loop are composed by three-Axis virtual flight motion simulator, simulation computer, load torque simulator, and visual simulation systems. Three-Axis Virtual Flight Motion Simulator are used to simulate the attitude of missile in simulation system with hardware-in-loop, so its performance influenced the result of simulation directly. This paper mainly analyzed the factors which influenced the performance of a three-Axis virtual flight motion simulator which we are used now in the lab, then analyzed the entire simulation system’s error caused by these factors through numerical simulation method. By analysis we can see that bandwidth is the main factor influenced the precision of simulation systems with hardware-in-loop, mechanical device installation error and measurement error may also cause some errors of the systems at the same time.