In order to guarantee the stable flight of a guided projectile, it is difficult to realize in-flight alignment for the micro inertial navigation system (MINS) during its short flight time. In this paper, a method based on changing acceleration using exponential function is proposed. First, double-vector observations were derived. Then the initial attitude for the guided projectiles was estimated by the regressive quaternion estimation (QUEST) algorithm. Further, the estimated errors were analyzed, and the reason for using the changing acceleration for the in-flight alignment was explained. A simulation and semi-physical experiment was performed to show the effectiveness of the proposed method. The results showed that the initial attitude error for the rolling angle was about 0.35°, the pitch angle was about 0.1° and the heading angle was about 0.6°, in which the initial shooting angle was between 15° and 55°. In future studies, the field experiments will be carried out to test the stability of the proposed in-flight alignment for guided projectiles.