The intricate nature of ships and floating structures presents a significant challenge for ship designers when determining suitable structural dimensions for maritime applications. This study addresses a critical research gap by focusing on a three-cargo hold model for a multipurpose cargo ship. The complex composition of these structures, including stiffening plates, deck plates, bottom plates, frames, and bulkheads, necessitates thorough structural analysis to facilitate effective and cost-efficient design evaluation. To address this challenge, the research utilises FEMAP-integrated NX NASTRAN software (2021.2) to assess hull girder stress. Furthermore, a novel approach is introduced, integrating the Design of Experiments (DOE) principles within Minitab 21.4.1 software to identify critical parameters affecting hull girder stress and production costs. This method determined the top five key parameters influencing hull girder stress: Hatch coaming plate, Hatch coaming top plate, Main deck plate, Shear strake plate, and Bottom plate, while also highlighting key parameters that impact production costs: the inner bottom plate, Inner side shell plate, Bottom plate, Web frame spacing, and Side shell plate. Ship design optimisation is then carried out by incorporating regression equations from Minitab software into the Non-dominated Sorting Genetic Algorithm II (NSGA-II), which is managed using Python software (PyCharm Community Editon 2020.3.1). This optimisation process yields a significant 10% reduction in both ship weight and production costs compared to the previous design, achieved through prudent adjustments in plate thickness, web frame positioning, and stiffener arrangement. The optimally designed midship section undergoes rigorous validation to ensure conformity with industry standards and classification society regulations. Necessary adjustments to inner bottom plates and double bottom side girders are made to meet these stringent requirements. This research offers a comprehensive framework for the structural optimisation of ship hulls, potentially enhancing safety, sustainability, and competitiveness within the maritime engineering industry.