It is essential for the innovation, transformation and industrial reform of the domestic shipbuilding industry to overcome the design challenges of large Liquefied Natural Gas (LNG) ships and thus solve bottleneck technologies. However, the large LNG ships generally adopt the design of double shafting with double shafting lines of inward inclination angles. This unique design results in an extremely complex flow field at the stern of the ship with increased lateral forces on the shafting, adversely affecting the safe and stable operation of the shafting. The calculation method for the shafting alignment is studied thoroughly by examining the hull deformation, propeller hydrodynamics and bearing oil film thickness of a large LNG double shafting ship. This method more truly reproduces the actual operating state of the shafting, improves the safety margin of the shafting, and obtains a forward-looking, feasible and stable calculation scheme for the dynamic alignment of the double shafting.