The Semi-Direct Injection (SDI) system has been shown to improve small engine efficiency and exhaust by utilizing a lean burn method. In order to better understand how to more readily utilize the control systems in SDI engine, the real-time operation of an SDI engine was modeled. A charging model was developed by using a filling-and-emptying model to simulate air exchange in an engine, including varying the intake manifold structure. A single-zone model was applied to a combustion model and the effects of air/fuel ratio and swirl ratio on combustion duration were also considered. The calculated results of the intake manifold pressure, heat release rate, and cylinder pressure were compared with the experimental data. The results of this study show that this modeling process approximates reality.