A numerical simulation was performed to investigate the pilot ignited natural gas combustion process in a direct injection natural gas engine. Various mixture distribution characteristics were compared in terms of the evolution of mixture equivalent ratio distributions and mixture concentration stratifications around top dead center (TDC). Based on above, the pilot injections were specially designed to investigate ignition core formation and its effects on natural gas combustion process. The result shows that pilot ignition sites have great impacts on pilot fuel ignition process and natural gas combustion process. The pilot ignition site on the region with rich NG/Air mixture is disadvantageous to the pilot fuel ignition due to a lack of oxygen, which is not beneficial to ignition core formation. Pilot ignition site on the relative leaner region adjacent to the rich NG/Air mixture is a better choice for pilot injection, as it is beneficial both to the pilot fuel ignition process and following combustion process. With various NG/Air mixture equivalent ratio distributions, different pilot ignited combustion processes were observed. In this study, three kinds of pilot ignited combustion processes were differentiated by the characteristics of ignition core formation, which were: (1) Single ignition source initiating the whole combustion, (2) sequential ignition of pilot fuel spray, (3) multi-ignition sites formed in pilot fuel spray. The first combustion process has the shortcoming of low combustion rate far from the ignition source, which leads to high UHC emission easily. The second and third combustion processes have lower UHC emission, as the reaction zones expand quickly within the combustion chamber. The results emphasize that both pilot injection and concentration stratification of NG/Air mixture need to be deliberately designed and organized to optimize the pilot ignited natural gas combustion process.