In this study, the split-channel supercharge and fuel-air mixing technology (SCS-FAM) is firstly proposed for large-bore ammonia (NH3)-hydrogen (H2) engine, which involves the separation of fuel and air intake ports to mitigate the risk of H2 backfire in intake system. We explored the activity stratification under different intake schemes and H2 blend ratios through simulation, as well as how it affects the NH3–H2 combined combustion characteristics including in-cylinder flow turbulence, temperature, concentration, and key intermediates distribution. The results show that in Scheme 2 when air entered the high swirl ratio intake 1 and fuel entered the low swirl ratio intake 2, a rich mixture was formed near the spark plug, accompanied by localized NH3 thermal reforming phenomena, which improved the activity distribution of H2. Additionally, the strong swirl promoted combustion in the squish zone and significantly shortened the post-combustion period. Scheme 2 achieved a higher indicated thermal efficiency (ITE) than Scheme 1 with a small amount of H2 addition, with the highest ITE of 42.1% obtained at 15 vol% H2 blend ratio. Notably, the addition of H2 promoted NH3 consumption and the generation of active radicals, resulting in reduced N2O emissions during the expansion stroke, but causing an increase in NO emissions.