Aiming at the position coupling, gyroscopic effect, and synchronized vibration caused by the unbalance mass in the magnetic bearing rotor, a linear active disturbance rejection notch decoupling control method is proposed. Firstly, a model with coupling and unbalanced vibration of the system was established. The terms of position coupling, gyroscopic effect, and unbalanced vibration in the system are estimated by Extended State Observer and the estimator is treated as the system disturbance to be compensated, then the radially existing coupled and unbalanced vibration systems are decoupled into four independent second-order series-integrated subsystems. The nonlinear state error feedback control law is designed to implement the decoupling control of each subsystem. For the problem of unbalanced vibration of the rotor after decoupling, the suppression method of the dynamic unbalanced force of the same frequency notch filter is designed, and then the closed-loop feedback structure of the new method is deduced, and its frequency characteristics are analyzed. Then the rules and principles of controller parameter selection are summarized using Bode diagram. The simulation results show that the designed linear active disturbance rejection notch decoupling controller not only achieves the decoupling control of the respective degrees of the magnetic bearing rotor but also suppresses the unbalanced vibration of the rotor. At the same time, it solves the influence of the gyroscopic effect on the control under the high-speed running of the magnetic bearing rotor.