The transfer alignment of SINS/GPS navigation system of a high-speed marine missile was investiga-ted. With the help of the big acceleration of a high-speed missile, the transfer alignment was changed into a three-time alignment. The azimuth alignment was coarsely finished in 10s in the first time alignment, the hori-zontal alignment was accurately and rapidly finished in the second time alignment, and the azimuth alignment was accurately finished in the third time alignment. Because the second time alignment and the third time align-ment were finished by GPS after the missile was launched, the horizontal alignment and the second azimuth a-lignment got rid of the influence of the warship body flexibility deforming. The precision and rapidity of the hori-zontal alignment were prominently increased due to the vertical launch of the marine missile with the big accel-eration. Simulation verifies the effectiveness of the proposed alignment method.