This paper was to address the shortcomings of current design practice to evaluate the stability of the shaft alignment for a 300,000 DWT Very Large Crude Oil Carrier. An enhanced approach using FE was applied to identify the influence of hull deformation on the alignment of the shafting system. The effectiveness of this method was demonstrated in comparison with Jack up technique. Analysis results showed that the hull deformation could be a key factor affecting the offset distortion of each bearing supporting the shaft line. Moreover, it was confirmed that the deformation pattern of cargo hold was opposite to the deformation of engine room structure when hull deformation occurred due to draught change of the case ship. As new research findings, they are believed to contribute significantly to the prevention of shaft damage associated with hull deformations, thereby improving the reliability of shaft alignment for similar types of vessels.