Abstract Due to the pressing issue of global warming, there has been a significant focus on zero- and low-carbon fuels globally. Among hydrocarbon fuels, methane is widely used in spark ignition engines due to its abundance and relatively low carbon footprint. However, to further reduce carbon emissions, interest is growing in the use of ammonia, a zero-carbon fuel, as a partial replacement for methane. Consequently, it is crucial to investigate the impact of ammonia addition on the performance of natural gas spark ignition engines. A key challenge in studying ammonia-methane engines is that the introduction of ammonia alters the formation mechanisms of nitrogen-based pollutants, resulting in the coupling of fuel-borne and air-borne nitrogen pollutants. As a result, research on the nitrogen-based emissions of ammonia-methane engines has been limited. This study addresses this issue by differentiating between atmospheric nitrogen and fuel nitrogen elements, effectively decoupling fuel-borne and air-borne nitrogen pollutants. This approach provides valuable insights into the effects of ammonia addition on the nitrogen-based pollutant characteristics of natural gas engines. The results indicate that ammonia addition introduces N2O, a species absent in pure methane engines. The N2O primarily originates from cold wall regions and the partial oxidation of ammonia released from engine crevices during the late oxidation process. Although NO remains the dominant nitrogen-based pollutant and the amount of N2O is small, the significant greenhouse gas potential of N2O warrants further attention. Furthermore, while ammonia addition increases the NO concentration in the burning zone, it slightly reduces the NO concentration at chemical equilibrium under stoichiometric conditions. As a result, engines operating with an ammonia energy substitution ratio of 0.4 exhibit lower NOx emissions compared to those fueled solely by methane. These findings underscore the need for further research into the combustion and emission characteristics of ammonia-methane spark ignition engines.