To address the issue of vortices generated during transonic operation in hydrogen fuel cell centrifugal compressors, a study was conducted based on experimental flow field data from high-speed foreign fluid machinery and RANS (Reynolds-averaged Navier-Stokes) theory. Numerical simulations of the flow field characteristics in the impeller passage under transonic conditions were performed using ANSYS CFX. The focus was placed on analyzing the flow field during boundary layer transition on transonic blades and optimizing the centrifugal blade structure. The results show as follows. At an impeller rotational speed of 120 000 r/min, the flow field was observed to operate in a transonic regime. Due to the interaction between shock waves and the boundary layer at the blade inlet, it was found that boundary layer separation was accelerated, and large-scale vortices were generated at the passage inlet. By introducing cylindrical vortex generators near the blade leading edge, the kinetic energy of the boundary layer fluid was enhanced, enabling improved resistance to flow separation. This modification resulted in suppressed boundary layer separation at the blade front, optimized flow control, and weakened large-scale vortex structures. Additionally, the velocity distribution uniformity within the flow field was improved, leading to reduced energy losses. A reduction of approximately 16.7% in the maximum pressure pulsation was achieved, which provides valuable insights and methodological guidance for transonic centrifugal impeller research.