Abstract: The effect of low Reynolds number on the flow instability mechanism of transonic compressor was studied numerically.The result shows that the radial vortex exists in the compressor inner flow field,which is formed from separation flow in the boundary layer transition zone.Under centrifugal force,radial vortex flows from blade hub to blade tip and converges at the blade tip flow field.As Reynolds number decreases,the effect range of radial vortex is extended,a bigger boundary layer separation zone is formed at the blade tip,which is decisive to the flow instability of transonic axial compressor before blockage zone due to shock and tip leakage flow is fully developed.