Aiming at the problems that the high-speed motor rotor of fuel cell air compressor is easy to be damaged due to high-speed instability and the accelerated wear of air bearing due to rotor overload, the rotor stress and critical speed of different rotor structures are studied by using the finite element method, and a hollow rotor structure with axially preloaded and fixed magnetic steel is presented. Then, taking an ultra-high-speed permanent magnet motor with the rated power of 35 kW and the peak speed of 100 000 r/min as an example, the advantages and disadvantages of different rotor structures in strength, critical speed, mass, moment of inertia, assembly manufacturability and reliability are compared and analyzed comprehensively. The comparison results show that although the new rotor structure is slightly inferior in rotor strength in comparison with several common rotor structures, it has great advantages in other aspects. Finally, an air compressor prototype is manufactured according to the new rotor structure, and experimental results show that the prototype can run stably at the speed of 100 000 r/min, which verifies the rationality of the new rotor structure.