Compression ignition engines will still be predominant in the naval sector: their high efficiency, high torque, and heavy weight perfectly suit the demands and architecture of ships. Nevertheless, recent emission legislations impose limitations to the pollutant emissions levels in this sector as well. In addition to post-treatment systems, it is necessary to reduce some pollutant species, and, therefore, the study of combustion strategies and new fuels can represent valid paths for limiting environmental harmful emissions such as CO2. The use of methane in dual fuel mode has already been implemented on existent vessels, but the progressive decarbonization will lead to the utilization of carbon-neutral or carbon-free fuels such as, in the last case, hydrogen. Thanks to its high reactivity nature, it can be helpful in the reduction of exhaust CH4. On the contrary, together with the high temperatures achieved by its oxidation, hydrogen could cause uncontrolled ignition of the premixed charge and high emissions of NOx. As a matter of fact, a source of ignition is still necessary to have better control on the whole combustion development. To this end, an optimal and specific injection strategy can help to overcome all the before-mentioned issues. In this study, three-dimensional numerical simulations have been performed with the ANSYS Forte® software (version 19.2) in an 8.8 L dual fuel engine cylinder supplied with methane, hydrogen, or hydrogen–methane blends with reference to experimental tests from the literature. A new kinetic mechanism has been used for the description of diesel fuel surrogate oxidation with a set of reactions specifically addressed for the low temperatures together with the GRIMECH 3.0 for CH4 and H2. This kinetics scheme allowed for the adequate reproduction of the ignition timing for the various mixtures used. Preliminary calculations with a one-dimensional commercial code were performed to retrieve the initial conditions of CFD calculations in the cylinder. The used approach demonstrated to be quite a reliable tool to predict the performance of a marine engine working under dual fuel mode with hydrogen-based blends at medium load. As a result, the system modelling shows that using hydrogen as fuel in the engine can achieve the same performance as diesel/natural gas, but when hydrogen totally replaces methane, CO2 is decreased up to 54% at the expense of the increase of about 76% of NOx emissions.