This study proposes a fuel supply system for dual-fuel propulsion engines using liquefied natural gas (LNG) and ammonia to control carbon emissions. The independent fuel supply system of LNG and ammonia is configured as a hybrid system. The operating pressure of the re-condenser is determined as a process variable according to the power consumption and flow rate of the non-condensable boil-off gas. The independent and hybrid systems are compared and evaluated through thermodynamic analyses, including specific power consumption (SPC) and exergy analyses, with respect to the fuel ratio and engine load. When the engine load is 100% in Case 1 for a 40% carbon reduction by 2030, the hybrid system exhibits an SPC reduction of 70% and exergy efficiency increase of 16% compared with the independent system.