Abstract: The electromagnetic bearing-flywheel rotor system generally adopts a differential control strategy, and there are two opposing electromagnetic coils in each degree of freedom for an electromagnetic bearing. The driving currents of the two electromagnetic coils are obtained by differential operation of the control current and the given bias current, where the bias current is the same, while the control current is equal in magnitude and opposite in direction. So when the drive current of the electromagnetic coils is small, the system will also generate additional power losses due to the presence of constant bias current. In order to solve this problem, a suspension control method is proposed based on adaptive bias algorithm, which is composed of two submodules: improved PID algorithm and adaptive bias algorithm. In the improved PID algorithm, the differentiator of the traditional PID algorithm is replaced by a velocity observer, and the improved PID algorithm is used to calculate the control current, so as to effectively suppress the interference of external noise. The adaptive bias algorithm calculates the bias current in real-time according to the vibration amplitude of the rotor and the control current, and then performs differential operations between the bias current and the control current to generate the driving current of the electromagnetic coils. Then the two electromagnetic coils generate control electromagnetic force to ensure the stable suspension of the flywheel rotor. With the help of system simulation and experiments, the vibration control performance of the control system, the driving current of the electromagnetic bearing, and the noise resistance of the system are analyzed. The results show that the control method proposed in this paper can effectively suppress the vibration of the electromagnetic bearing-flywheel rotor system, and has the characteristics of low power loss and strong anti-noise interference ability.