A novel design procedure of internal model controller based on the Double-Decomposition (DD), which includes the Full Rank Decomposition (FRD) and Singular Value Decomposition (SVD), is proposed for the multivariable system with multiple time-delay plant. In the controller design process, the Reflexive Generalised Inverse Matrix (RGIM) based on FRD is used to replace the generalised inverse matrix to design the internal model controller; improved filter based on SVD is introduced into the design process. In the FRD process for a non-square system, the Effective Relative Gain Array (ERGA) is applied to select the linear independent column. After model reduction for the internal model controller, the expression of the controller is obtained. Then the square system and the non-square system are taken as examples. The simulation results show the effectiveness of the proposed approach for the multivariable system with the multiple time-delay plant.