Hydrogen-based fuels are potential candidates to help international shipping achieve net-zero greenhouse gas (GHG) emissions by around 2050. This paper quantifies the environmental impacts of liquid hydrogen, liquid ammonia, and methanol used in a Post-Panamax container ship from 2020 to 2050. It considers cargo capacity changes, electricity decarbonization, and hydrogen production transitions under two International Energy Agency scenarios: the Stated Policies Scenario (STEPS) and the Net Zero Emissions by 2050 Scenario (NZE). Results show that, compared to the existing HFO ship, hydrogen-based propulsion systems can decrease cargo weight capacity by 0.3 % to 25 %. In the NZE scenario, hydrogen-based fuels can reduce GHG emissions per tonne-nautical mile by 48 %–65 % compared to heavy fuel oil by 2050. Even with fully renewable hydrogen-based fuels, 18 %–31 % of GHG emissions would still remain. Using hydrogen-based fuels in internal combustion engines requires attention to minimize environmental trade-offs.