This paper presents a novel magnetically levitated centrifugal hydrogen recirculation pump (MLCHRP) designed for proton exchange membrane fuel cells (PEMFCs). Compared to traditional hydrogen recirculation pump, the MLCHRP offers significant advantages, including no lubrication, no mechanical friction, and active vibration suppression. However, the compact design of the pump imposes constraints on the load capacity of the active magnetic bearings (AMBs). As a result, the rotor is more susceptible to instability when subjected to unbalanced disturbance forces. This paper details the structure of the MLCHRP and provides an analysis of the basic model for unbalanced disturbance forces. A method for suppressing these unbalanced disturbances is proposed, utilizing a Linear Extended State Observer (LESO) combined with Parallel Peak Filters (PPF). The impact of this approach on system stability is thoroughly examined, and the effectiveness of the proposed method for unbalanced disturbance suppression is experimentally validated. The experimental results show that the peak-to-peak displacement of the rotor decreased by 80%. Additionally, the synchronous component in the rotor's displacement FFT was reduced by 6 dB (from -19.2 dB), and the second harmonic component decreased by 23.8 dB (from -23.7 dB). Finally, aerodynamic performance tests confirm that the MLCHRP meets the application requirements of actual PEMFCs system.