A control-oriented two-zone charge mixing model is developed to simplify, but to describe mixing of fresh charge and residual gas during the intake stroke. Engine valve timing has a strong influence on the realization of stable homogeneous charge compression ignition (HCCI), since it affects turbulent flow that promotes mixing of fresh charge and residual gas. Controlled auto-ignition of a HCCI engine is achieved by good mixing of fresh charge and residual gas. Therefore, it is useful to develop a mixing model that can be executed in real-time to help extend the operational range of HCCI. For model derivation, the cylinder volume is artificially divided into two zones with a fictitious divider between them. First, the mixed zone consists of fresh charge induced by opening intake valves and some residual gas transferred from the unmixed zone. They are assumed to have been mixed homogeneously so that cold fresh charge gains thermal energy from hot residual gas. Second, the unmixed zone contains the rest of hot residual gas. Mass transfer between them which is forced by a fluid jet is directed from the unmixed zone to the mixed one. Based on the definitions of two zones and interaction between them, a two-zone charge mixing model is derived. To investigate phasing effects of valve timing on charge mixing, comparative simulation was carried out with different valve timings. For experimental validation and calibration of the proposed model, optical engine tests were performed with an infrared (IR) camera, together with GT-power simulation. From good agreement between the model temperature and the estimated temperature from IR images, the model turns out to be useful to describe mixing of fresh charge and residual gas.