In this paper, a numerical study to simulate and analyze the combustion process occurred in a compressed natural gas direct injection (CNG-DI) engine by using a multi-dimensional computational fluid dynamics (CFD) code was presented. The investigation was performed on a single cylinder of the 1.6-liter engine running at wide open throttle at a fixed speed of 2000 rpm. The mesh generation was established via an embedded algorithm for moving meshes and boundaries for providing a more accurate transient condition of the operating engine. The combustion process was characterized with the eddy-break-up model of Magnussen for unpremixed or diffusion reaction. The modeling of gaseous fuel injection was described to define the start and end of injection timing. The utilized ignition strategy into the computational mesh was also explained to obtain the real spark ignition timing. The natural gas employed is considered to be 100% methane ($CH_4$) with three global step reaction scheme. The CFD simulation was started from the intake valves opening until the time before exhaust valves opening. The results of CFD simulation were then compared with the data obtained from the single-cylinder engine experiment and showed a close agreement. For verification purpose, comparison between numerical and experimental work are in the form of average in-cylinder pressure, engine power as well as emission level of CO and NO.