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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.