<p>Centrifugal separation machinery, especially those with vertical rotor structures and ball joint constraints, face significant operational stability challenges due to shaft center position and vibration issues, as well as strong lateral cross-coupling characteristics from their complex support structure. To address these challenges, this study proposes a novel real-time control method for the center position of a centrifuge rotor. The method integrates a variable step-size least mean square notch filter (VSLNF), a tracking differentiator (TD), and an all-coefficient adaptive control (ACAC) based on a characteristic model. The method dynamically updates the characteristic model coefficients to adapt to system changes, achieving precise shaft center control. The VSLNF removes synchronous frequency vibrations, the TD handles complex dynamics, and the ACAC adapts to varying conditions. This approach is particularly suitable for centrifuges with complex support structures, differing from conventional magnetically levitated rotor systems. The numerical study establishes a finite element model of the centrifuge and designs an adaptive controller to adjust the rotor position in real-time. The combination of ACAC with VSLNF and TD allows for effective vibration control under both constant and variable speed conditions, significantly reducing high-speed vibrations after crossing critical speeds. Experimental results demonstrate that the method effectively controls rotor displacement and reduces vibrations, offering a novel solution for vibration control in industrial rotating machinery with significant engineering application value.</p>