Aiming at the problems that the electromagnetic levitation system is easily affected by external disturbances and the inherent contradiction of the integer order PD in the traditional linear active disturbance rejection control, this paper proposes a fractional order linear active disturbance rejection control method. The linear extended state observer is used to estimate the total disturbance of the system in real time, and a fractional order differential operator is introduced into the position loop control law. By utilizing the characteristic that its order can be continuously adjusted within the interval (0, 2), the requirements of phase and amplitude in the frequency domain are flexibly adapted. Theoretical analysis shows that fractional-order linear active disturbance rejection controller can simultaneously enhance the disturbance suppression ability in the low-frequency band and suppress the high-frequency noise amplification effect. Simulation and experimental results show that, compared with linear active disturbance rejection control, fractional-order linear active disturbance rejection controller, reduces the position deviation by 48.72%, shortens the adjustment time by 80.28%, and can effectively deal with stronger disturbances and improve the tracking accuracy, significantly enhancing the anti-interference and tracking performance of the system.