Abstract: In order to solve the problem of matching data dropout of transfer alignment which can cause big estimation error or divergence of the alignment filter, a ship-borne alignment method based on improved unscented Kalman filter (UKF) was proposed, in which a control variable that can adjust the filtering update process according to the situation of measurement data dropout was introduced. Under the proposed scheme, the boundedness of the estimation error can be guaranteed. Moreover, the new alignment method can acquire accurate estimate of attitude misalignment in the situations of different matching data dropout rates. Finally, the effectiveness is demonstrated by the simulation study.