For the next stage of Homogeneous Charge Compression Ignition (HCCI) engine researches, the development of an engine controller, taking account of dynamics is required. The objective of this paper is to develop dynamic multi input and multi output HCCI engine models and a controller to deal with variable valve lift, variable valve phase, and fuel injection. First, a physical continuous model has been developed. This model mainly consists of air flow models, an ignition model, and a combustion and mechanical model of the engine. The flow models use a receiver model on volumetric elements such as an intake manifold and a valve flow model on throttling elements such as intake valves. Livengood-wu integration of Arrhenius function is used to predict ignition timing. The combustion duration is expressed as a function of ignition timings. The effects of start timing of fuel injection, intake valve phase, intake valve lift, exhaust valve phase, and exhaust valve lift on in-cylinder gas pressure were investigated in both calculations and experiments; the engine model shows good agreement with empirical results. Next a discrete non-linear engine model was developed, from which a linear model was deduced mathematically by Taylor expansion. Finally, transient response of the constructed calculation models were investigated.