Traditional inertial navigation error models based on the earth coordinate system are not suitable for space applications. An overall design of integrated navigation system for space applications is given. The inertial navigation error model is derived based on the inertial coordinate system (J2000), The Integrated navigation system is designed by the mathematical model of GPS, SINS with CNS and the extended Kalman filter. There are two simulation in interruption of continuous signals and signal simulation of two models. The results show that the simulation system can satisfy the spacecraft in orbit of the navigation performance requirements, the design of spacecraft navigation system has a certain reference value.