Actuation force precision is important for precision motion control of magnetic suspension system. In order to realize the motion control of magnetic levitation system, it is assumed that the electromagnetic force changes instantaneously with the change of the input current. However, due to the hysteresis effect of the electromagnetic material, the current output from the power amplifier in the traditional control method cannot compensate for this in time. In this paper, a single-degree-of-freedom (SDOF) magnetic suspension motion control system is designed with a Hall sensor to measure the magnetic field strength for flux feedback control. By adding an inner flux feedback loop to the traditional position feedback control, the position-flux feedback control is realized, and the hysteresis effect of electromagnet is compensated to improve the electromagnet force accuracy and position control accuracy. Proportional Integral (PI) control is applied for flux feedback control. Proportional Derivative (PD) control strategies is applied for position feedback control with a Extended state observer (ESO) to reduce the effect of other unknown perturbations and improve the robustness of the system. The results show that the flux feedback control has faster response speed, better control accuracy and dynamic performance than the traditional control methods.