In this paper a statistical physics based mean value model (MVM) is introduced for a heated intake homogeneous charge compression ignition (HCCI) engine based on a previously developed crank angle resolved model [1] and validated. In this HCCI engine, regulation of combustion timing is based on manipulating the cylinder charge temperature through the cold and hot throttle actuators. This two-input and single-output (TISO) system offers an input redundancy which is utilized to separately account for the fast fuel loading changes and the slower variations in the hot inlet (heated air) temperatures via appropriate actuator authority allocation. All the available experimental data sets suggest that the combustion duration Δθ comb between the crank angle of 10% and 90% fuel burned (θ CA10 and θ CA90 ) can be used as the combustion timing regulation variable. This choice is shown to guarantee both combustion stability and fuel efficiency in terms of covariance of indicated mean effective pressure (IMEP) and indicated specific fuel consumption (ISFC) respectively. Simulations of the linear controller with the nonlinear plant demonstrate the closed loop performance.