Previously, the authors have proposed the concept of piston trajectory-based homogeneous charge compression ignition (HCCI) combustion control enabled by a free piston engine and shown the effects of variable piston trajectories on the start of combustion timing, heat loss amount and indicated output work. In order to realize this new control in practical applications, a control-oriented model with reduced chemical kinetics has to be developed. In this paper, such a model is presented and is compared to two existing models: a simplified model using a global reaction and a complex model including detailed chemical reaction mechanisms. A cycle separation method is employed in the proposed model to significantly reduce the computational time and guarantee the prediction accuracy simultaneously. A feedback controller is also implemented on the control-oriented model to control the HCCI combustion phasing by varying the trajectories. The simulation results show that the combustion phasing can be adjusted as desired, which demonstrates the effectiveness of the piston trajectory-based combustion control.