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This paper describes the development and application of a synthesis‐level multidisciplinary design and optimization (MDO) method for multihull ships. This method is unique in utilizing advanced multi‐objective optimization methods, neural network (NN)‐based response surface methods (RSM), and in its broad scope, integrating powering, stability, seakeeping, hullforms definition, structural weights, and cost and payload capacity into a single design tool. This MDO method is developed in the context of a multilevel hierarchy system approach where the results of the synthesis level optimization can be used for subsystem optimization and overall coordination of multilevel design system. NN‐based RSM for seakeeping and powering is developed and used in the optimization process. This RSM approach moves the computational cost of such performance evaluations out of the optimization cycle, substantially reduces the optimization cost, and allows for using results of physics‐based methods, such as advanced computational fluid dynamics, at the synthesis‐design level of design hierarchy. Details of these methods are delineated and multi‐objective optimization results are presented in the form of Pareto optimum solutions for multihull ship concepts such as trimaran sealift support ships and catamaran high‐speed connector ships.