High-speed magnetically suspended Turbo Molecular Pumps (TMPs) have been widely used in industrial applications for their high energy density, micro-vibration, and no lubrication requirements. However, the Active Magnetic Bearing (AMB) system will lose magnetic force once the main power fails, which may cause severe damage to the rotor and stator systems. In this study, an improved Power Failure Compensation Control (PFCC) method based on Average Power Balance Control (APBC) was proposed. First, a motor energy feedback circuit was designed. Then, a nonlinear controller consisting of double control loops was proposed, of which the fast inner current loop used Sliding Mode Control (SMC) and the outer voltage loop used APBC. The Lyapunov function was structured and analyzed to ensure system stability. Finally, a platform based on the high-speed magnetically suspended TMP was built. Several experimental results verify that the proposed PFCC method has fast response and robustness; meanwhile, the touchdown speed of the rotor is reduced to 3 900 r/min from the rated speed of 21 000 r/min with a higher energy conversion efficiency of up to 96.6%, which greatly improves the safety of the AMB system.