During transfer alignment navigation information transferred MINS(master inertial navigation system) to SINS(slave inertial navigation system) has a changed time delay. The changed time delay degrades the performance of transfer alignment. This paper proposes an adaptive filter that estimates covariance of a time delay in real-time using residual of measurements. The performance of the adaptive filter is compared with that of the EKF(extended Kalman filter) in case of transfer alignment for vertical launcher in the ship. The results show that proposed method is more effective than EKF in estimating attitude errors.