In the context of global trade and environmental concerns, this research focuses on examining the influence of the principal dimensions of a container feeder vessel whose propulsion has been modified to operate with green methanol. Methanol emerges as a sustainable marine fuel, reducing emissions and dependence on fossil fuels. The study comprehensively examines the structural challenges posed by container ships, with a particular focus on torsional stresses and hydroelasticity effects. A significant novelty of this study is the inclusion of a comparative structural analysis evaluating how changes in the vessel’s main dimensions impact its structural response. This analysis sheds some light on crucial insights into the effects of structural modifications required for accommodating these changes, ensuring the structural strength of these vessels. The research also underscores the impact of permanent and transient springing and whipping phenomena on fatigue damage. The study’s significance lies in its role in the ongoing transition to sustainable maritime transportation, as it not only examines structural challenges but also provides solutions for achieving an optimal structural configuration in this new era of environmental responsibility.