Bearing damages by shaft misalignment have frequently been happened in marine ships. Specially. after stern tube bearing damage and failure for large crude oil carriers have been reported several times. However. the bearing reaction of the after stern tube bearing cannot be measured by jack-up test due to the hull structure condition. Therefore, when the jack-up test is used for the bearing reaction measurements, the bearing reaction for the after stern tube bearing obtained from the theoretical calculation method have to be used. In this paper, the shaft alignment on the large oil crude carrier is theoretically calculated and the differences between the calculated and actual installed bearing reaction values are compared. The bearing reactions for forward stern tube bearing and intermediate bearing are calculated by the simple formula using the strain gauge bending moments obtained from the measurements. Their reliability is confirmed by comparing the bearing reactions from jack-up test and the bearing reaction for after stern tube bearing is calculated by the same test. Also, the bearing reactions on the after stern tube bearing, forward stern tube bearing and intermediate shaft bearing under all operating conditions are calculated by using the bending moments obtained from the measurements and it is confirmed that the differences of the bearing reaction for all operating conditions are caused from hull deflection. The results of this study should prove useful for the future projects of the alignment calculation including the hull deflection effectiveness.