This paper deals with the transfer alignment problem of SDINS(StrapDown Inertial Navigation System) subjected to roll and pitch motions of the ship. In order to reduce alignment errors induced by ship body flexure, a linearized error model for the velocity and attitude matching transfer alignment system is first derived by linearizing the nonlinear measurement equation with respect to the dominant y axis component and defining the flexure state of random constant type. And then a robust state estimation scheme is introduced to account for modeling uncertainty of the flexure. By interpreting the simulation results and comparing with the velocity and DCM(Direction Cosine Matrix) partial matching method, it is shown that the proposed method is effective enough to improve the azimuth alignment performance.