In order to meet the navigation requirements of high-accurate and high-reliable for hypersonic vehicles, a quadratic intelligent optimization method which can identify error parameters of strap-down inertial navigation system(SINS) in launch inertial coordinate system is proposed. The error compensating model and the complete nonlinear navigation model of the SINS are established, which can provide accurate model basis for optimization calculation. Based on information of the SINS/GPS/CNS integrated navigation system, the optimization model of gyro errors and the optimization model of accelerometer errors are built, and the quadratic intelligent strategy is adopted to estimate error parameters of the SINS. Firstly, error parameters of gyro are identified and compensated by using the particle swarm algorithm. On this basis, the error parameters of accelerometer are identified by using the particle swarm algorithm. The simulation results show that the quadratic optimization identification method can high-accurate identify the error parameters of the SINS online based on information of the integrated navigation system and the nonlinear optimization model, and the relative errors of optimization parameters of gyro and accelerometer are within 20%, and the navigation precision of the hypersonic vehicle is improved significantly.