This paper presents a strategy and an algorithm for levitation control of an over-actuated passive maglev tray system. The passive maglev tray system has more actuators than its degrees of freedom. The actuators of the system are switching when the tray travels longitudinally. Furthermore, the levitation forces of the actuators are non-homogeneous because the actuation devices are not in the moving platform. These characteristics make a limit in using conventional control approaches for levitation. For smooth actuator switching, the actuator force generation should be dependent on longitudinal positions of the tray. To enable constant pose tracking, this research introduces a control strategy and a control algorithm based on integral controllers on virtual variables. The states of the tray are estimated using a Kalman filter and fed to the proposed controller. The performances of the proposed control strategy and the algorithm are validated through tests.