The invention relates to a method for controlling the structural modal vibration of a dual-frame magnetic levitation control moment gyroscope (CMG). On the basis of establishing a nominal model of an electromagnet rotor system, a sine-swept excitation mode is adopted to perform the identification of frequency domains on an electromagnet rotor and measure the disturbance of system parameters, the properties of structural vibration modality and the high-frequency unmodeled dynamics of an electromagnet rotor model; and a comprehensive robust control method of a structural singular value mu is utilized to select a weighting function and inhibit the structural modal vibration. The method belongs to the technical field of aerospace control, and can be used for inhibiting the structural modal vibration of the dual-frame magnetic levitation CMG.