In order to improve the survival ability and rapid response ability of the carrier craft, a new rapid transfer alignment method of the strapdown inertial navigation system (SINS) on a rocking base is put forward. In the method, the aircraft carrier does not need any form of movement. Meantime, interfering motions such as rolling, pitching, and yawing motions caused by sea waves are effectively used. Firstly, the deck exure deformation model is made. Secondly, the state space model of transfer alignment is presented. Finally, the feasibility of this method is validated by the simulation. Simulation results show that the misalignment angle error can be estimated and reach an anticipated precision-0.2 mrad in 5 s, while the deck deformation angle error can be estimated and reach a better precision-0.1 mrad in 20 s.