Homogeneous charge compression ignition (HCCI) is a promising internal combustion engine concept, but suffers from its high sensitivity to operation conditions and disturbances, such as the intake temperature fluctuation, the load fluctuation or the in-cylinder temperature distribution variation. In this paper, a novel control method is proposed for a port-fuel-injected stoichiometric HCCI engine equipped with variable valve actuation (VVA). A first principle model is developed for controller synthesis with intake valve closing (IVC), exhaust valve closing (EVC), and injected fuel quantity as inputs and combustion timing (CA50), Gross IMEP and Lambda as outputs. The proposed method combines the features of model-based feedforward, decoupling, and active disturbance rejection control (ADRC), named MDDC for short, where the easily modeled cross-coupling and disturbances are compensated directly, while all the remaining uncertainties are estimated and mitigated in real time by ADRC. MDDC is tested and compared with model predictive control (MPC) on a Simulink/GT-power platform. Initial results show that the proposed method has adequate performance and a remarkable advantage in robustness against the changes in engine speed (from 1200 r/min to 1800 r/min), intake temperature(from 30°C to 0°C) and coolant temperature (from 90°C to 75°C). Furthermore, it only needs a rough, low order model and very little computation in the engine control unit (ECU), making it a strong candidate among competing solutions for the HCCI combustion control.