A SINS/GPS online alignment method based on the square root cubature Kalman filter and initial attitude estimation algorithm is proposed in this paper. The square root cubature Kalman filter is constructed to handle the nonlinear measurement model of the initial attitude which is represented with Rodrigue parameter, and the attitude transformation matrix at the current time is obtained. The semi physical simulations of the guided weapon and the vehicle system are carried out. The results show that the online alignment can be finished within 25 s with the proposed method.The simulation results of short range guided weapon show that the yaw and pitch angle errors are within 0.1° and the roll angle errors are within 0.3°. The simulation results of low cost vehicle navigation system show that the yaw angle errors are within 0.2° and the pitch and roll angle errors are within 1°, which can meet the alignment requirements of guided weapons and low cost civil vehicles.