Abstract: When dealing with engine room layout optimization problems, existing optimization algorithms have problems such as extremely low proportion of feasible solutions and converge difficulties. Therefore, research on a multi-objective intelligent optimization system for ship engine room layout is carried out. A fractional-step multi-objective optimization system is proposed, conducted in two steps: First, using the equipment layout sequence as design variables, the NSGA-II algorithm and the mixed packing algorithm proposed in this paper are employed to solve the integer programming problem and complete the initial layout scheme selection. Second, based on the initial layout scheme, with the equipment spacing and aisles width as design variables, obtain the optimal layout scheme after optimization. Finally, the improved optimization system is applied to optimize the equipment layout in a local area of a ship's engine room. The results show that the optimization method can achieve a significant improvement in partial performance objectives on the basis that the optimization objectives are not lower than the manually designed layout. The optimization effect of overall space utilization is significant, with an optimization range of 33.36%, the optimization range of maintenance efficiency is 17.18%, and the maximum width of the channel and maintenance space is optimized by 0.47% compared with the prototype. The study demonstrates that the fractional-step optimization method is feasible and applicable, greatly enhancing the efficiency and effectiveness of ship engine room layout optimization, and it provides an effective solution for the intelligent layout design of the power compartment.