A modified two-degrees-of-freedom ( M-TDOF) internal model control ( IMC) method is proposed for non-square systems with multiple time delays and right-half-plane (RHP) zeros. In this method, pseudo-inverse is introduced to design the internal model controller, and a desired closed-loop transfer function is designed to eliminate the unrealizable factors of the derived controller. In addition, set-point tracking and load-disturbance rejection of each process are separately controlled by two controllers. The simulation results show that in addition to high decoupling performance and robustness, the proposed control method also effectively improves load-disturbance rejection and simultaneously optimizes the input tracking performance and disturbance rejection performance by selecting the parameters of controllers. Furthermore, the higher tolerance of model mismatch is achieved in this paper.