An air-independent propulsion system containing fuel cells is applied to improve the operational performance of underwater vehicles in an underwater environment. Fuel-reforming efficiently stores and supplies hydrogen required to operate fuel cells. In this study, the applicability of a fuel-reforming system using various fuels for underwater vehicles was analyzed by calculating the fuel and water consumptions, the amount of CO2 generated as a byproduct, and the amount of water required to dissolve the CO2 using aspen HYSYS (Aspen Technology, Inc., Bedford, MA, USA). In addition, the performance of the fuel-reforming system for methanol, which occupies the smallest volume in the system, was researched by analyzing performance indicators such as methanol conversion rate, hydrogen, yield and selectivity, and reforming efficiency under conditions at which pressure, temperature, steam-to-carbon ratio (SCR), and hydrogen separation efficiency vary. The highest reforming efficiency was 77.7−77.8% at 260 °C and 270 °C. At SCR 1.5, the reforming efficiency was the highest, which is 77.8%, and the CO2 generation amount was the lowest at 1.46 kmol/h. At high separation efficiency, the reforming efficiency increased due to the reduction of reactants, and a rate at which energy is consumed for endothermic reactions also decreased, resulting in a lower CO2 generation amount.