The disturbance suppression of magnetic levitation turbomolecular pumps is a critical problem in industrial applications. This work addresses the stability control of high-speed magnetic levitation turbomolecular pumps with shock-excited disturbance. A disturbance suppression method based on improved linear extended state observer is proposed to attenuate the impact of external low-frequency disturbing force on a magnetic levitation turbomolecular pump. Firstly, a linear extended state observer of an active magnetic bearing is obtained by analyzing the rotor dynamics model. Then, the detailed descriptions of external disturbance suppression method using linear extended state observers and adaptive notch filters are discussed for the system. The boundary condition of the parameters of the improved linear extended state observer is determined. The root loci of the closed-loop system with improved linear extended state observers is also investigated. Finally, simulation and experimental results on a magnetic levitation turbomolecular pump show the applicability of the proposed method. The results show that the proposed method can attenuate the rotor vibration displacement caused by impact by 46.9%.