Homogeneous Charge Compression Ignition (HCCI) is a promising concept for combustion engines to reduce both emissions and fuel consumption. HCCI combustion control is a challenging issue because there is no direct initiator of combustion. Variable Valve Timing (VVT) is being used in SI engines to improve engine efficiency. When VVT is used in conjunction with HCCI combustion it is an effective way to control the start of combustion. VVT changes the amount of trapped residual gas and the effective compression ratio for each cycle both of which have a strong effect on combustion timing in HCCI engines. To control HCCI combustion, a physics based control oriented model is developed that includes the effect of trapped residual gas on combustion timing. The control oriented model is obtained by taking a physics based model of the reaction kinetics and transient dynamics and systematically reducing the model using simplification of reaction mechanisms. This method allows different fuels to be incorporated using a standard methodology. The reduced order model consists of these five stages: intake, compression, combustion, expansion and exhaust. This model fills the gap between complex models with highly detailed chemical kinetics and simple black box dynamic models that have been used in model based control.