Flutter is a highly destructive aeroelastic problem in modern compressors, which hinders the improvements of aero-engine performance and reliability. Because the aerodynamic work is mainly concentrated in the blade tip region, the tip clearance which is associated to the complex tip clearance flow has a considerable effect on the flutter stability. In this paper, in order to investigate the influence mechanism of the tip clearance on the flutter stability at different nodal diameters (ND), a series of compressor models were established with different tip clearances based on a transonic compressor rotor. The aerodynamic damping at each ND is obtained by influence coefficient method (ICM), while phase-shifted boundary method (PSB) is adopted to analyze the influence of the tip clearance on the flutter stability at different NDs. The results indicate the worst flutter stability for each tip clearance always appears at ND=1, where the aerodynamic damping exhibits a nonmonotonic trend of increasing first and decreasing thereafter along with the rising tip clearance. Two kinds of action are exerted by the tip clearance flow on the flow structures to alter the flutter stability: one is the tip clearance vortices which is generated on the suction side and impinge on the pressure side; the other is the interference of tip clearance vortices to the shock wave and to the flow separation. Besides, the influence of the changing aerodynamic coupling effect makes the above action bring about more drastic fluctuations to the unsteady pressure. At larger NDs, the unsteady pressure amplitude and phase fluctuate more sharply for larger tip clearances. Therefore, diverse change trends of the aerodynamic damping with the increasing tip clearance appear at different NDs, while the impingement of tip clearance vortices on the adjacent pressure side has a constantly stabilizing effect at different NDs.