Energy efficiency is the main direction of innovation in today’s shipping industry. In particular, the Ship Energy Efficiency Design Index (EEDI), which came into effect by IMO on January 1, 2013, has pushed energy efficiency innovation to a whole new level. Since the introduction of marine shaft generator in the 1980s, it has been gradually applied to large container ships after successive major changes and innovations. However, there are no application case of shaft generator on a full-scale Very Large Crude Carrier (VLCC) due to the limitations imposed by many factors such as space and speed. The world’s first VLCC equipped with the shaft generator is optimized with consideration of the influences of the shafting torsional vibration equipment, bearing load distribution, machinery space layout and stern shaft extraction, etc. The shaft system of the VLCC is optimized and designed from three aspects of shafting arrangement, shafting torsional calculation and shafting alignment calculation. A feasible, efficient and forward-looking low-cost optimization design scheme of the shafting is then obtained by adjusting the number, material and diameter of the shafting, and the height of the main engine.