Abstract: For the vibration control of the magnetically suspended rotor system under no speed sensor condition, a speed adaptive auto balancing algorithm based on second order generalized integral-frequency locked loop (SOGI-FLL) was proposed. Firstly, the principle of zero current and zero bearing force control was analyzed based on the unbalanced dynamic model of the magnetically suspended rotor. Then, an adaptive zero current control strategy was constructed based on the notch channel and frequency estimation characteristics of SOGI-FLL, and its phase shift version with was further designed. On this basis, the stability of the closed-loop system with the algorithm was analyzed. Finally, simulation and experiment results prove that the algorithm has good speed adaptive estimation performance, and can effectively suppress the transmitted vibration to the base from the rotor system.