This paper presents the excitation force control of double electro-dynamic shaker system. The multiple-input multiple-output (MIMO) control of excitation forces of shakers on the thin plate structure is performed both for linear combination of sinusoidal signals and magnitude varying sinusoidal signals. For the MIMO control purpose, inverse transfer function based controller is implemented on the feedback control loop. Inverse-transfer functions of electro-dynamic shaker system are easy to obtain via system identification method because of their linear system property. In addition, this type of controller is reliable and suitable to use in MIMO system control since it is able to eliminate the input signals’ coupling effect on the output. Through the experiments, it is verified that the designed controller is capable of control the excitation forces of two shakers within the 1Hz, 30Hz frequency range.