The Global Shipping industry is responsible for transporting 90% of global commerce and is responsible for 3% of global greenhouse gas (GHG) emissions. Addressing this, the International Maritime Organization (IMO) aims to reduce GHG emissions from international shipping by 40% by 2030 and achieve net zero by 2050. This study explores Low Temperature-Proton Exchange Membrane Fuel Cell (LT-PEMFC) hybrid energy systems as a potential solution to reduce shipping emissions. Emphasizing the operational zero-emission capability of PEMFC fueled by hydrogen, the research scrutinizes the emission intensity from hydrogen production and the impact of component degradation on hybrid system efficiency and hydrogen consumption. The research pivots around optimizing the design and operation of ship hybrid energy systems to minimize costs while considering well-to-wake (WTW) emissions and component lifetime. It investigates two hybrid configurations: PEMFC/Li-ion battery (LIB) and Diesel Generator (DG)/PEMFC/LIB. Employing a Mixed Integer Linear Programming approach for component modeling, the study conducts a two-stage analysis: design optimization considering various hydrogen sources and plant lifetime estimation focusing on PEMFC and battery degradation. Initial findings reveal that system design costs do not significantly differ across hydrogen grades. The DG/PEMFC/LIB configuration emerges as cost-effective, reducing CAPEX by 62.8% compared to the PEMFC/LIB setup. Carbon Capture and Storage (CCS) hydrogen grades strike a balance between cost and emission reduction, notably cutting emissions by up to 85% in the PEMFC/LIB configuration at a 27% OPEX increase. Lifetime estimation highlights the effectiveness of a hierarchical optimization method in mitigating PEMFC voltage loss and extending component lifespan, albeit with increased battery cycling aging. The study underscores the importance of selecting the appropriate hydrogen grade and operational strategies to enhance the sustainability and economic viability of maritime hybrid energy systems, aligning with IMO’s emission reduction goals.