A SINS/CNS/SAR integrated navigation system suitable for cruise missile is designed in this paper. Aiming at the requirements of high precision and autonomy of the navigation system and the characteristics of uniform speed and constant height flight of cruise missile, the engineering practicability of the project is highlighted. The nonlinear modeling is adopted for the SINS/CNS/SAR integrated navigation and the nonlinear UKF method is used to perform the filtering of the subfilters. The nonlinear model and filter method are more practical, so the system accuracy is improved. In the information fusion process among the subfilters, the federal filter based on the information allocation factor is selected to adjust the system in realtime, which greatly enhances the fault tolerance and realtime performance of the system. A new method for computing observability is proposed and the observability computation is simplified. The digital and hardware in the loop simulation experiments show that the integrated navigation system is very suitable for the high altitude long endurance flight environment of cruise missiles. The integrated navigation system is not only suitable for cruise missiles, but also has great engineering value for some other long endurance aircrafts, such as UAVs, and has great engineering application value.