To approach realization of Homogeneous Charge Compression Ignition (HCCI) combustion without external combustion ignition trigger, it is necessary to construct HCCI engine control system. In this study, HCCI research engine equipped with the EGR passage for external EGR and the two-stage exhaust cam for exhaust rebreathed. This system can control the mixing ratio of four gases (air, fuel, rebreathed EGR gas, external EGR gas) of in-cylinder by operating four throttles and fuel injection duration while maintaining acceptable pressure rise rate (PRR) and cycle-to-cycle variation of Indicated Mean Effective Pressure (IMEP), closed-loop control system designed by applying feedback variables (equivalence ratio, combustion-phasing, IMEP) for feedback control.Those control inputs (four throttles and fuel injection) has correlation mutually, control inputs cause interference, response become low and hunching occurs. Therefore, model-based control system with modern control theory which is multi-inputs-multi-outputs system has been constructed to control HCCI combustion. For easily constructing linear- quadratic-integral (LQI) controller, discrete model was designed by discretizing 1 cycle of HCCI combustion into 6 points that represent the control-oriented description of the HCCI engine as a thermodynamic system. Although the results from discrete model nearly match with that of experiments near the base condition, the errors became large as the control input separates from base conditions. Furthermore, we tried linearization of discrete model implementing Taylor expansion for LQI control system.