When flexible rotors approach critical speeds, resonance phenomena caused by natural frequency characteristics significantly amplify vibration amplitudes. This amplification can induce rotor–stator contact friction through bearing interactions, potentially leading to system destabilization. Therefore, active control strategies are essential for vibration mitigation during critical speed transitions to ensure operational stability. Based on mechanical principles, this study establishes a Timoshenko beam-based finite element model for magnetically levitated rotors and conducts dynamic characteristic analysis. To overcome computational complexities from high-order finite element formulations, prolonged simulations and modal coordinate transformations were applied, achieving accurate model order reduction. For improved vibration suppression during critical speed traversal, we propose a model-assisted linear extended state observer (MA-LESO) integrated active disturbance rejection control (ADRC) framework. This approach enables precise estimation and compensation of high-frequency disturbances through synergistic fusion of physical models and observer methodologies. Numerical simulations demonstrate that the proposed control strategy achieves 35.59% reduction in peak vibration displacement at critical speeds and 45.85% attenuation of low-frequency oscillations.