The final goal of shift alignment design is that the bearing reaction forces or mean pressures are within design boundaries for various service conditions of a ship. However, it is found that calculated bearing load can be substantially variable according to the locations of the effective support points of after sterntube bearing which are determined by simple calculation or assumption suggested by classification societies. A new analysis method for shaft alignment calculation is introduced in order to resolve these problems. Key concept of the new method is featured by adopting both nonlinear elastic and multi-support elements to simulate a bearing support Hertz contact theory is basically applied for nonlinear elastic stiffness calculation instead of the projected area method suggested by most of classification societies. Three loading conditions according to the bearing offset and the hydrodynamic moment and twelve models according to the locations of the effective support points of sterntube bearings are prepared to carry out quantitative verifications for an actual shafting system of 8000 TEU class container vessel. It is found that there is relatively large difference between assumed and calculated effective support points.