Ammonia is employed as the carbon-free fuel in the future engine, which is consistent with the requirements of the current national dual-carbon policy. However, the great amount of NOx and unburned NH3/H2 in the exhaust emissions is produced from combustion of ammonia and is one kind of the most strictly controlled pollutants in the emission regulation. This paper aims to investigate the NOx and unburned NH3/H2 generative process and emission characteristics by CFD simulation during the engine combustion. The results show that the unburned ammonia and hydrogen emissions increase with an increase of equivalence ratio and hydrogen blending ratio. In contrast, the emission concentrations of NOx, NO, and NO2 decrease with the increasing of equivalence ratio, but increase with hydrogen blending ratio rising. The emission concentration of N2O is highly sensitive to the O/H group and temperature, and it is precisely opposite to that of NO and NO2. Moreover, by a trade-off between NOx and unburned NH3/H2 emissions, it is difficult to simultaneously achieve low emissions for both. Thus, the engine should be operated at stoichiometry or slightly lean combustion strategy, and with a blending ratio of around 0.1, which is more appropriate. Moreover, in order to keep the lower emissions relying solely on in-cylinder combustion control strategy is insufficient for ammonia-hydrogen fueled engines, and the development of specialized aftertreatment system is crucial and urgent.