The output compensation and feedback compensation are two traditional methods of the initial alignment strap down inertial navigation system (SINS). The degree of observability is the standard to evaluate the state of Kalman filter. For the purpose to improve the alignment accuracy, the effect of the degree of observability and the feedback compensation on the SINS alignment accuracy is analyzed. The conclusion shows that the state estimation result is related to the compensation method, and a proper feedback quantity can lead to a batter result. Based on this conclusion, a considerable adaptive feedback compensation method based on observability analysis is proposed. Finally, the method is proved to be efficient on improving the alignment accuracy by a simulate experiment in which three methods are used to do the initial alignment on the ground stationary base.