In this study a semi-reduced reaction scheme developed previously was used to derive a 26 step reduced mechanism, using the sensitivity approach and the steady state approximation (QSS) with Chemkin code. This 26 step model has been implemented in a CFD combustion code (STAR-CD/Kinetics) to study combustion process in homogeneous charge compression ignition (HCCI) engines. The first results obtained have confirmed the very rapid combustion phase and fast heat release with completely homogeneous mixtures, for a wide range of operating conditions. This numerical approach has been used first to study the effects of natural thermal stratification when the mixture is initially homogeneous. In a second step, the different possible methods to control the heat release rate have been studied. The stratification with several homogeneous regions of different composition is shown to be very efficient; the limits of this process are discussed.