In this study, we propose an Overlay security mechanism, which is secure and practical, based on Space Operating System (SpaceOS). Firstly, the system security domain is divided, and the requirement of security mechanism is defined. The design idea of security mechanism is put forward, and the security requirement is proved by formal method. Then, the feasibility of the technology is explained by Overlay file system, and the security mechanism is applied to SpaceOS. Finally, the performance test, security test, and practicability test are carried out. The test shows that the Overlay security mechanism is secure and practicable. It has little effect on the speed of the SpaceOS has practical value.