The electromagnetic bearing–flywheel rotor system typically uses a differential control approach, featuring two opposing electromagnetic coils for each degree of freedom of an electromagnetic bearing. Differential operation of the control current and a specified bias current determines the driving currents of the electromagnetic coils, with the bias current remaining constant while the control current exhibits equal magnitude and opposite direction. However, when the electromagnetic coils’ drive current is small, the system incurs additional power losses owing to the constant bias current. To address this issue, this study introduces a suspension control method leveraging an adaptive bias algorithm. The proposed suspension control method comprises two submodules: an enhanced Proportion Integral Differential (PID) control algorithm and an adaptive bias algorithm. In the enhanced PID algorithm, a velocity observer replaces the differentiator of the conventional PID algorithm, effectively mitigating the impact of external noise. The adaptive bias algorithm calculates the bias current in real time based on the rotor’s vibration amplitude and the control current. Differential operations between the bias current and the control current then yield the driving current for the electromagnetic coils. The two electromagnetic coils subsequently generate a control electromagnetic force, ensuring the stable suspension of the flywheel rotor. Through system simulations and experiments, the vibration control performance of the proposed control system, the driving current of the electromagnetic bearing, and the system’s noise resistance were evaluated. The findings demonstrate that the control method effectively suppresses vibrations in the electromagnetic bearing–flywheel rotor system, exhibiting low power loss and strong noise resistance.