Abstract: The application of wireless power transfer (WPT) technology has been extended to workshop AGV, electric vehicles, and many other fields. However, in the process of technology application, due to the limitation of monomeric power capacity, the overall power transmission capacity is limited to a certain extent. The WPT system with multiple excitation units (MEU) can effectively improve the power transmission capacity of the system, give more power regulation freedoms and reduce monomeric voltage and current stress. However, the cross coupling among multiple coils and high system order greatly increases the difficulty of controller design. Based on the characteristics that the mode energy of the multi-excitation-unit WPT system is concentrated in a very few modes, a controller matrix method based on model inverse was proposed. At the same time, this paper also provided a general framework for the controller design of multi-input multi-output (MIMO) WPT system. This method can be directly extended to multi-degree-of-freedom WPT systems with multiple transmitting coils and multiple receiving coils. Finally, the effectiveness of the control method was verified by experiment.