In this paper, the real-time control system of missile and rocket projectile flight simulation is improved to ensure accurate timing and data synchronization, which is important to improve the fidelity of flight simulation system. At present, the most widely used Windows operating system has poor real-time performance. As a control system of missile and arrow flight simulation, there will be uncertainties in control flight and other problems. In this paper, RTX real-time control system is introduced under the kernel of Windows operating system, which improves the timely control performance of Windows and is verified by experiments. The results show that the design method can meet the real-time control requirements of missile flight simulation under Windows operating system.