To meet the miniaturization requirements of a reaction flywheel for small satellites, a reaction flywheel system using the axial flux permanent magnet motor based on a Printed Circuit Board (PCB) stator was proposed and the winding layout form for the PCB stator winding was researched as well. According to the system design and manufacturing requirements, a combination of theoretical and finite element analysis was applied to the illustration of generating mechanism of the reverse torque in the spiral winding. The effects of spirally type and waveform type PCD stator windings on the flywheel system performance were also analyzed, respectively. Finally, the performance of flywheel system prototypes with two forms of stator windings was tested on the ground. The results indicate that the driven motor with the waveform PCB stator winding has reduced its power consumption by 26.2% than that with spirally winding when the flywheel works at a rated speed of 5 000 r/min, meanwhile its electromagnetic efficiency is also reduced by 0.8%. The experimental results verify the correctness of theoretical analysis and simulation results, and provides an important reference for the engineering applications of the axial flux permanent motors with PCB stator windings.