The performance of actively controlled magnetic bearings is greatly degraded if subjected to unpredictable disturbances or system dynamic variations. This paper present an adaptive synchronization control on a magnetically suspended rotor system for disturbance rejection and plant variation compensation. The rotor system consists of a rotating disk mounted on a shaft which is actively positioned in the radial directions via two magnetic bearings at both ends. Under the synchronizing control, four displacements of shaft along bearing axes are coordinated such that the disturbed displacement can promptly be recovered with those undisturbed in a complementary way. Such motion synchronization requires strict regulation and adaptation through four local controllers with an adaptive feedforward control scheme. The local controllers can be linked by the coupling law, in which an error along one bearing axis can affect overall control loop of four axes. Two control algorithms are developed under the biaxial and quadaxial synchronization conditions, and their adaptation laws are optimized in an attempt to minimize the adaptation errors. Simulations of disturbance rejection responses will also be presented.