In this paper, a simplified Cubature Kalman Filter (SCKF) is proposed to reduce the computation load of CKF, which is then used as a filter for transfer alignment of shipboard INS. CKF is an approximate Bayesian filter that can be applied to non-linear systems. When an initial estimation error is large, convergence characteristic of the CKF is more stable than that of the Extended Kalman Filter (EKF), and the reliability of the filter operation is more ensured than that of the Unscented Kalman Filter (UKF). However, when a system degree is large, the computation amount of CKF is also increased significantly, becoming a burden on real-time implementation in embedded systems. A simplified CKF is proposed to address this problem. This filter is applied to shipboard inertial navigation system (INS) transfer alignment. In the filter design for transfer alignment, measurement type and measurement update rate should be determined first, and if an application target is a ship, lever-arm problem, flexure of the hull, and asynchronous time problem between Master Inertial Navigation System (MINS) and Slave Inertial Navigation System (SINS) should be taken into consideration. In this paper, a transfer alignment filter based on SCKF is designed by considering these problems, and its performance is validated based on simulations.