As sustainable green fuels for heavy-duty engines, using hydrogen doping with ammonia helps to mitigate greenhouse gas emissions. Based on the background of hydrogen production from ammonia reforming, the combustion and emission characteristics of hydrogen-doped ammonia engines are studied. By employing 3D-CFD numerical simulation, this study systematically explores the combined effects of the ignition timing, hydrogen energy ratio (HER), and equivalence ratio (Φ) on the premixed combustion and emission performances of ammonia–hydrogen blends. The findings indicate that at the operating conditions of HER = 4% and Φ = 1.0, the indicated mean effective pressure (IMEP) reaches its maximum at −40 °CA aTDC, with the indicated thermal efficiency (ITE) reaching 48.2%. However, to mitigate knock hazards, the ignition timing should be adjusted to −37.5 °CA aTDC. With HER increasing from 4% to 25%, the flame propagation velocity is markedly improved, and the combustion duration is notably reduced. As the equivalence ratio rises from 0.8 to 1.0, the combustion intensity is strengthened while the proportion of indicated work declines. Notably, the lean burn condition (Φ = 0.8) exhibits no knock risk and achieves the highest ITE (49.2%). In terms of emission characteristics, advanced ignition timing, higher HER, and lower equivalence ratio all promote NO_X formation. In contrast, N₂O emissions decrease as the combustion temperature rises and the combustion duration shortens. Unburned NH₃ is mainly distributed in the low-temperature areas inside the cylinder, and its emission amount decreases with the improvement of combustion completeness.