In order to estimate and rectify SINS misalignment angle during missile powered-flight phase, the limitation of Kalman filter algorithm in which the misalignment angles are treated as state variable was analyzed, and the navigation error spread equations were derived in launch-point inertial coordinate, and also proposed is a new method that estimates the misalignment angles as invariable parameters based on least square method. The simulation results indicate that the new method based on least squares has less computation, easier for practical applications, performs much more quickly and steady than Kalman filter, and the off-line calculation with real flight data further indicates that the proposed algorithm is effective.