The increasing demands for reducing fuel consumption and emissions in contemporary technology solutions lead to the use of more sensors, actuators, and control applications. With this increasing engine complexity, the feedback design is complex due to the coupling between inputs and combustion parameters. To be able to design the controller systematically, model predictive control (MPC) comes to the scope because of its advantages in the design of multi-input multi-output (MIMO) systems, especially with its constraints handling ability and performance in simultaneously optimizing the engine fuel efficiency and emission reduction. Multi-injection is one of the promising techniques for achieving better engine performance. In this work, post-injection control is implemented utilizing MPC MIMO strategy with the target of exploring the possibility of reducing emissions and improving engine efficiency by controlling post-injection duration and injection timing. The workflow of the MPC controller design from control-oriented model (COM) establishing to MPC problem formation and solution methodology is discussed in this work. Moreover, one contribution from this work is the different implementation angle when compared with the state-of-the-art approaches, where the MPC controller is implemented purely by Matlab Simulink to enable the rapid control prototyping design. The simulation result demonstrated the ability of the controller's tracking performance and showed a preliminary step towards the nonlinear combustion model-based multi-injection MPC design. The systematic model-based controller framework developed in this work can be applied to other control applications and enables a fast path from design to test.