Abstract: Researched on the moving base transfer alignment of the ship synthesize navigation information system on the shipborne weapons associating integrated navigation information system of the warship, put forward flexure and time delay as system state, and gave system state equation and measurement equation. This paper used federal filter as the information fusion algorithm for transfer alignment program, variable of system equation was analyzed by method of PWCS, the velocity and attitude matching sub-filters equation and major filter equation were deduced. At last, this method was simulated and the result of simulation showed azimuth misalignment used federated filter was better than traditional filter 20 percent; application for federated filter could resolve the problem of transfer alignment for FOG SINS about the ship is effectively.