It has been shown that using fuel additives play an important role in enhancing the combustion characteristics in terms of efficiency and emissions. In addition, free piston engines have shown capable in reducing energy losses and presenting more efficient and reliable engines. In this context, the objective of the present work is to investigate the effect of using hydrogen as a fuel additive in natural gas homogeneous charge compression ignition free piston engine. To this aim, two models have been iteratively coupled: the combustion model that is used to calculate the heat release of the combustion and the scavenging model that is employed to determine the in-cylinder mixture state after scavenging in terms of its homogeneity and species mass fractions and to obtain the finial pressure and temperature of the in-cylinder mixture. In the former model, the 0-D approach through Cantera toolkit has been considered due to the fact that homogeneous charge compression ignition combustion is very rapid and the fuel-air mixture is well-homogenous, whereas in the latter model, 3-D-CFD approach through AN-SYS FLUENT software is considered to ensure precise calculations of the species exchange at the end of each engine cycle. The effect of hydrogen as a fuel additive has been quantified in terms of the combustion characteristics (e. g., ignition delay, heat release rate, engine overall efficiency and emissions, etc.). It has been shown that hydrogen addition reduces ignition delay time, decreases the in-cylinder peak pressure, while allowing the engine to operate with higher mechanical efficiency as it has high heat release rate, increases the NOx emission levels of the engine, but decreases the CO levels