With the development of China's army modernization, the aircraft carrier weapon has been fielded as a strategic weapon. Because of the wave, the sea breeze effect causes the carrier deck swing and sway. This brings difficulty to carrier aircraft inertial navigation system SINS initial alignment. To solve this problem, it was inferred that aircraft carrier rocking shaking produced by the interference of acceleration in inertial space is the harmonic form and generally smaller than the acceleration due to gravity amplitude. So the gravity information can be got from output of acceleration after smoothing, and the process of acceleration due to gravity point's vector of analytic coarse alignment and fine alignment algorithm was put forward. Theoretical analysis and simulation results show that the moving base SINS alignment method can effectively solve the initial alignment of the aircraft carrier in the state of the ship mooring.