This paper addresses the control strategy for the suppression of maglev vehicle-bridge interaction resonance, which worsens the ride comfort of vehicle and degrades the safety of the bridge. Firstly, a minimum model containing a flexible bridge and ten levitation units is presented. Based on the minimum model, we pointed out that magnetic flux feedback instead of the traditional current feedback is capable of simplifying the block diagram of the interaction system. Furthermore, considering the uncertainty of the bridge’s modal frequency, the stability of the interaction system is explored according to an improved root-locus technique. Motivated by the positive effects of the mechanical damping of bridges and the feedback channels’ difference between the levitation subsystem and the bridge subsystem, the increment of electrical damping by the additional feedback of vertical velocity of bridge is proposed and several related implementation issues are addressed. Finally, the numerical and experimental results illustrating the stability improvement are provided.