The free-piston engine is a type of none-crank engine that could be operated under variable compression ratio, and this provides it flexible fuel applicability and low engine emission potential. In this work, several 1-D engine models, including conventional gasoline engines, free-piston gasoline engines and free-piston hydrogen engines, have been established. Both engine performance and emission performance under engine speeds between 5–11 Hz and with different equivalent ratios have been simulated and compared. Results indicated that the free-piston engine has remarkable potential for NOx reduction, and the largest reduction is 57.37% at 6 Hz compared with a conventional gasoline engine. However, the figure of NOx from the hydrogen free-piston engine is slightly higher than that of the gasoline free-piston engine, and the difference increases with the increase of engine speed. In addition, several factors and their relationships related to hydrogen combustion in the free-piston engine have been investigated, and results show that the equivalent ratio φ=0.88 is a vital point that affects NOx production, and the ignition advance timing could also affect combustion duration, the highest in-cylinder temperature and NOx production to a large extent.