The precise control of centrifugal hydrogen compressor (CHC) driven by high-speed permanent magnet synchronous motor (PMSM) is the key to the stable and efficient operation of hydrogen fuel cell (HFC). In this paper, an adaptive current deviation decoupling control (CDDC) strategy based on variable step size affine projection algorithm (VSS-APAs) is proposed to solve the high-speed PMSM control problem caused by current cross-coupling and parameter perturbation under complex operating conditions. Firstly, the step size is dynamically adjusted by VSS-APA through a normalized gradient descent to respond to system fluctuations, achieving rapid parameter identification during dynamic changes and accurate tracking in steady states. Secondly, stator inductance, magnetic flux linkage, stator resistance, and disturbance torque are identified in two-time-scale based on the characteristics of parameter changes, overcoming the rank deficiency in motor mathematical equations. Finally, utilizing online-identified motor parameters, the gains of the CDDC are adjusted, and compensation is applied for back electromotive force (BEMF) and disturbance torque, thereby ensuring the control accuracy of the motor under parameter perturbations and system disturbances. Experimental results demonstrate that the proposed method enhances the responsiveness and accuracy of the control strategy through efficient parameters identification. Consequently, it guarantees high-efficiency and stable performance of the CHC across different working conditions, markedly advancing the overall functionality and dependability of hydrogen energy system.