The co-combustion of traditional methane gas and alternative fuels importance to reduce emissions in combustion has increased in recent years. The literature proves the successful operations of ammonia and hydrogen as diesel engine fuels. However, there is not sufficient information about the combustion of methane along with ammonia and hydrogen. In this study, the effects of the combustion of methane-hydrogen and methane-ammonia-hydrogen fuel mixture on system performance and emissions are numerically investigated. Firstly, the effects of methane and 5%, 10%, and 15% hydrogen mixture are investigated. Then, methane and 5% fixed hydrogen ratio with 5% ammonia, 10% ammonia, and 15% ammonia mixtures are examined. The numerical model is validated against the literature data using the Sandia D model with a difference of 5.9% at x/d = 0.5. As a result of the study, 15% hydrogen addition to methane increased the maximum combustion chamber temperature by 100 K. However, with the addition of 15% of ammonia, the temperature is dropped by 200 K and the peak temperature location is slightly shifted away from the injection point. A 10% enhancement of hydrogen content rate will cause a 28% increase in thermal NOX emission and a 10% increment in the ammonia content of the fuel blend has caused to 3000 ppm enhancement in NOX emission. With the addition of %5, 10%, and %15 ammonia mass fraction to methane and hydrogen blend fuel at the axial location of x/d = 0.444, the NOx emission production rate has been increased by 1970, 3010, and 3790 ppm, respectively. In addition, the 15% hydrogen addition to methane (85% methane/15% hydrogen) and 5% hydrogen plus 15% ammonia addition to methane (80% methane/5% hydrogen/15% ammonia) reduced the CO2 emission by 30.7% and 14% compared to neat methane (100% methane) combustion. To sum up, this study shows that the use of methane-ammonia-hydrogen as a diesel engine fuel reduces combustion emissions. © 2023 Hydrogen Energy Publications LLC