Ship's subdivision arrangement is a multi-objective combinatorial optimization problem with multiple nonlinear constraints. This study focuses on finding a methodology for ship's subdivision arrangement that can guarantee ship's offshore sequential ballast water exchanging (SBWE) performances in the preliminary design stage. A mathematical model is built using minimizing trims and hull girder longitudinal bending moments and shearing forces occurred in the SBWE as the objectives, and the multiple safety criteria of the SBWE as the constraints. The longitudinal lengths of the ballast water tanks (BWTs) are taken as design variables that will alter within a reasonable length range. An elitist nondominated sorting genetic algorithm (NSGA-II) is utilized to perform the optimization, in which the nondominated sorting mechanism is employed to handle the multiple objectives, and the constraint-domination principle is utilized to handle the multiple constraints. A special crossover operator called the dispersion apportioned allelic (DAA) crossover is introduced to perform the reproduction of the special problem. A real case study of the subdivision arrangement based on the SBWE of a 50,0000WT double hull product tanker is conducted to demonstrate the feasibility and effectiveness of the proposed approach.