In transfer alignment of airborne weapon, wing's flexure deformation has a significant impact on the alignment accuracy of slave SINS. Based on the analysis of alignment errors caused by the flexure deformation, an alignment filter with lower dimensionality, which employed “velocity + attitude" match scheme, was designed so as to meet the engineering requirement in the stage of the transfer alignment. In addition, the computational complexity was analyzed to evaluate the efficiency of transfer alignment filter. According to the alignment simulation, the results show that the proposed 17-dimensional Kalman filter can converge in 4~6s and deduce the computational complexity significantly.