This paper describes a control-oriented charge mixing and Homogeneous Charge Compression Ignition (HCCI) combustion model, where the in-cylinder charge is divided into the well-mixed and unmixed zones as the result of charge mixing. Simplified fluid dynamics is used to predict the residual gas fraction at the intake valve closing, which defines the size of the unmixed zone, during real-time simulations. The unmixed zone size not only determines how well the in-cylinder charge is mixed, which affects the start of HCCI combustion, the peak in-cylinder pressure and also the temperature during the combustion process. The developed model was validated in the HIL (hardware-in-the-loop) simulation environment. The HIL simulation results show that the proposed charge mixing and HCCI combustion model provides better agreement with these of the corresponding GT-Power than the previously developed one-zone model.