Ammonia is a zero-carbon candidate fuel for the decarbonization of internal combustion (IC) engines. A concern when using ammonia in IC engines is the increased emissions of nitrogen oxides (NOX), due to the additional nitrogen in the ammonia molecule. Compared to conventional petroleum such as gasoline and diesel, ammonia combustion adds the fuel NOX formation mechanism in addition to the original thermal NOX generation pathway, which further complicates the NOX emission characteristics of ammonia engines. Decoupling fuel NOX and thermal NOX helps to increase the understanding of the formation and evolutionary characteristics of nitrogen oxides occurring inside ammonia engines, but the available literature lacks studies in this respect. The purpose of this study is to fill this research gap and to propose a methodology for decoupling fuel NOX and thermal NOX. In brief, an artificial elemental nitrogen is applied to the Zeldovich mechanism and to the diatomic nitrogen in the combustion air, which allows the formation of NOX from the elemental nitrogen in the ammonia fuel to be separated from the NOX formed from the nitrogen in the air. A three dimensional (3D) computational fluid dynamics (CFD) model demonstrates the effectiveness of this approach and investigates the spatial and temporal distribution characteristics of thermal NOX and fuel NOX in the turbulent combustion field of ammonia engines. The in-cylinder activity analysis suggests that this separation of the NOX formation mechanism slightly alters the nitrogen-based chemistry, which is unavoidable. However, this approach still allows a reasonable characterization of the formation and evolution of fuel NOX and thermal NOX. The simulations show that fuel NOX is formed during ammonia oxidation because fuel NOX is an intermediate species, while thermal NOX has a high concentration in the burned zone because it is related to the temperature and the residence time of nitrogen at that temperature, both of which are expected and support the successful decoupling of fuel and atmospheric nitrogen. In addition, nitrous oxide (N2O) emissions come from the fuel NOX mechanism and are mainly distributed along the liner walls as it is formed by partial oxidation of ammonia released from the crevices during the late oxidation process. Moreover, the concentrations of both thermal and fuel-based nitrogen monoxide vary with the chemical equilibrium that changes with piston motion, and their concentrations are always comparable. As a result, combustion strategies for ammonia internal combustion engines needs to consider both thermal and fuel NOX reduction mechanisms, where the main difficulty is the N2O reduction. Catalytic combustion mode may be a viable strategy to improve the oxidation efficiency of the ammonia fuel trapped in the crevice and reduce N2O emissions in the cylinder.