The interaction of natural gas fuel manifold injection with the in-cylinder flow field, and the combustion behavior of an HCCI engine is numerically investigated by using numerous capabilities of multi-dimensional computational fluid dynamic (KIVA-3VR2) code coupled with detailed chemical kinetics. A validating oxidation reaction mechanism that mainly consisted from 314 elementary reactions among 52 species is employed to simulate the whole engine physicochemical process including the intake flow interaction with natural gas port fuel injection, the homogeneity of the gas fuel and the air during suction and compression strokes, autoignition and combustion process. The simulation problem of the gaseous fuel injection by using the original KIVA spray sub-model is solved by implementing a new modification into the original KIVA sub-routines to enable multiple inlet conditions through the use of regions. Each region has the same or different inlet conditions to permit the simulation code work probably. To overcome the challenges of autoignition timing and combustion phasing over a wide range of speeds and loads in practical CNG fuel in the application of HCCI engines we used hydrogen additives to the initial natural gas/air mixture. The optimal dose of hydrogen mole fraction is selected from the results of a Zero-Dimensional thermodynamic model. This model has been employed because the 3D-CFD results indicated that the fuel/air mixture is exactly perfect homogenous in the case of manifold fuel supply. However, the HCCI combustion is characterized by a flameless combustion in which a great amount of combustion spots in the whole chamber ignited simultaneously. The spots consume all the fuel mixture in a few crank angle degrees and the hydrogen gas in the mixture increases both of its number, its size, and advancing its occurrence time to produce higher combustion and emissions behavior. In addition, the simulation results indicated that formaldehyde and hydroxyl radical formation were considered as the most important species at low temperature oxidation and the hydrogen addition aids their formation.