In order to realize the coordinated control of the peak pressure and combustion phase of Homogeneous Charge Compression Ignition (HCCI) engine, this paper build a two input and two output physical model about the peak pressure and combustion phase, based on the shaver' residual-affected HCCI engine model and adding in the constant wall temperature heat transfer model suitable for HCCI combustion. Meanwhile the accuracy of the model have been verified. By using model predictive control theory, the cooperative control system of pressure and combustion phase of is designed. With variable valve timing (VVA) as control method, through the coordinated simulation experiment of GT-power and Matlab/simulink, the corresponding control effect can be obtained. The result shows that the physical-based model can satisfy the engine control demand. At the same time the MPC controller realized the collaborative control of the pressure and combustion phase with the control accuracy of and, response time of about 6 ∼ 7 engine cycle.