Due to the long distance between ship's integrated guidance information and ship's guided weapon, ship's deflection, information delay and non-synchronization have great influence on the accuracy of transfer alignment between master and sub-inertial guidance. Based on the deformation model of large ships, ship deflection, measurement delay and other relevant variables are included in the equation of state, which can significantly reduce the influence of deflection and delay on the transfer alignment accuracy. A sequential Kalman filter is designed to estimate the sub-inertial navigation attitude based on the non-synchronous measurement information. The simulation results show that the proposed method can meet the requirements of high accuracy and rapidity of shipborne guided weapon transfer alignment and has engineering application value.