Transfer alignment is greatly affected by lever arm effect in complex sea conditions, which is mainly reflected in the divergence degree of misalignment angle and the duration of alignment. In order to research the influence of different sea conditions on the lever arm effect, a ship six-degree-of-freedom model is established based on the idea of separated modeling, and an equivalent lever arm effect model is built on that basis. In simulation process, velocity matching transfer alignment is adopted in the equivalent lever arm effect model, and Kalman filter, Butterworth low-pass filter compensation and computational compensation methods are applied in comparative analysis. The simulation results show that the fifth grade sea state is the highest sea state grade for transfer alignment. The simulation results provide a theoretical basis for practical training, combat and mission execution, and also provide guidance for ship safety and the safety of carrier-based aircraft take-off and landing training.