This paper proposes SDINS(strapdown inertial navigation system) transfer alignment method for vertical launcher using an adaptive filter in the ship. First, the velocity and attitude matching transfer alignment method is designed to align SDINS for vertical launcher. Second, the adaptive filter is employed to estimate measurement noise variance in real time using the residual of measurements. Because it is difficult to decide measurement noise variance when noise properties of the ship SDINS are changed. To verify its performance, it is compared with the EKF(Extended Kalman filter) using uncorrect measurement variance. The monte carlo simulation results show that proposed method is more effective in estimating attitude angle than EKF.