To meet the lightweight design requirements of ship composite structures, this paper proposes a multi-objective optimization method for composite laminate layup. The method integrates the NSGA-II algorithm with the micromechanical Voigt-Reuss model and classical lamination theory. Furthermore, a novel tiered constraint strategy, tailored to the loading characteristics of ship structures, is introduced for the first time in the industry, successfully achieving the multi-objective (dual-objective) optimization of laminate layups. Taking a 40-layer carbon-fiber laminate as an example, the optimized design achieves a 14.6% increase in stiffness and a 98% satisfaction rate of manufacturing constraints compared to conventional methods. Finite-element verification under clamped boundary conditions shows a 32% reduction in maximum stress and a 12% increase in the first-order natural frequency. The application of this method to a high-speed composite catamaran demonstrates that the optimized hull-girder design leads to a 10% reduction in deflection and a 15.6% decrease in the fiber stress utilization factor in longitudinal strength calculations. This study provides a valuable reference for advancing ply-optimization design techniques for ship composite structures.