In order to verify the performance of SINS/BDII integrated navigation system, a method based on the flight control simulation system to generate the trajectory is adopted. The flight control simulation software is designed by Visual C++ programming language and flight control principle. The non-commutative error of rotation is effectively compensated by the double sub-sample rotation vector algorithm. The SINS/BDII integrated navigation system Kalman filter is designed by indirect filtering method. The verification results show that the SINS and integrated navigation system algorithms is correct under simulated flight conditions. The trajectory generation method has engineering application value.