In this paper, the detailed chemical kinetics was coupled with the three-dimensional CFD code to study the combustion process in HCCI engines. A detailed hydrocarbon oxidation reaction mechanism (89 species, 413 reactions) for high octane fuel was constructed and then used to simulate the chemical process of the ignition, combustion and pollutant formation under HCCI conditions. The three-dimensional FIRE/CHEMKIN model was validated using the experimental data from a Rapid Compression Machine. The simulation results show good agreements with experiments. Finally, the improved three-dimensional CFD code was employed to simulate the intake, spray, combustion and pollutant formation process of the gasoline direct injection HCCI engine with two-stage injection strategy. The models account for intake flow structure, spray atomization, spray/wall interaction, droplet evaporation and gas phase chemistry in complex multi-dimensional geometries. The calculated results show the periphery of fuel-rich zone formed by the second injection which ignited first and worked as an initiation to ignite the surrounding lean mixture zone formed by the first injection. The results provide a detailed insight into the processes governing combustion and pollutant formation in the HCCI engine.