Hydrogen serves as an optimal fuel for engines. Pure hydrogen engines do not generate carbon monoxide and hydrocarbon emissions; instead, they encounter significant nitrogen oxide emissions. Inner-engine control and outer-engine control are two methods to reduce NOx emissions. Outer-engine control primarily mitigates NOx emissions by selective catalytic reduction (SCR), a process that has been extensively researched. Nevertheless, there is a paucity of research about NOx emission regulation in pure hydrogen engines via internal engine management. This work utilised the closed homogeneous reactor (CHR) in Chemkin Pro to model the primary NOx emission control within pure hydrogen engines. The findings indicate that single exhaust gas recirculation (EGR) reduces NOx emissions by 45.3% at an EGR ratio of 20%, suggesting that the reduction in NOx emissions is not substantial. Nonetheless, EGR combined with lean burn reduces NOx emissions by 96.31% at a λ of 1.4 and an EGR ratio of 20%, resulting in ultra-low NOx emissions from pure hydrogen engines. In comparison to single EGR and EGR combined with lean-burn, SNCR is more effective for NOx emission control. An NH3 ratio of merely 10% can reduce NOx emissions by 96.32% in pure hydrogen engines, whilst a 15% NH3 ratio can attain zero NOx emissions in pure hydrogen engines without necessitating a high λ value or EGR ratio. It is essential to precisely regulate the NH3 ratio in the cylinder; otherwise, residual NH3 may be generated, leading to environmental pollution.