Configuring green power transmissions for heavy-industry marines is treated as a crucial request in an era of global energy and pollution crises. Following up on this hotspot trend, this paper examines the effectiveness of a modified optimization-based energy management strategy (OpEMS) for a dual proton exchange membrane fuel cells (dPEMFCs)-battery-ultra-capacitors (UCs)-driven hybrid electric vessels (HEVs). At first, the summed power of the dual PEMFCs is defined by using the equivalent consumption minimum strategy (ECMS). Accordingly, a map search engine (MSE) is proposed to appropriately split power for each FC stack and maximize its total efficiency. The remaining power is then distributed to each battery and UC using an adaptive co-state, timely determined based on the state of charge (SOC) of each device. Due to the strict constraint of the energy storage devices’ (ESDs) SOC, one fine-corrected layer is suggested to enhance the SOC regulations. With the comparative simulations with a specific rule-based EMS and other approaches for splitting power to each PEMFC unit, the effectiveness of the proposed topology is eventually verified with the highest efficiency, approximately about 0.505, and well-regulated ESDs’ SOCs are obtained.