The integrated control of a homogenous charge compression ignition (HCCI) combustion phasing, load, and exhaust aftertreatment system is essential for realizing high-efficient HCCI engines, while maintaining low hydrocarbon (HC) and carbon monoxide (CO) emissions. This paper introduces a new approach for integrated HCCI engine control by defining a novel performance index to characterize different HCCI operating regions. The experimental data from a single cylinder engine at 214 operating conditions is used to determine the performance index for a blended fuel HCCI engine. The new performance index is then used to design an optimum reference trajectory for a multi-input multi-output HCCI controller. The optimum trajectory is designed for control of the combustion phasing and indicated mean effective pressure (IMEP), while meeting catalyst light-off requirements for the exhaust aftertreatment system. The designed controller is tested on a previously validated physical HCCI engine model. The simulation results illustrate the successful application of the new approach for controller design of HCCI engines.