To realize the processing demands of the sapphire wafer surface with scratch-free and nano-scale roughness by mechanical polishing, a novel flexible polishing plate was developed by using soft unsaturated resin. The surface characteristics, material removal rate, and residual stress of the sapphire wafer after the flexible polishing process have been compared with those of the sapphire wafer after the rigid polishing process. Both theoretical and simulation analysis results show that the abrasive particles in the flexible polishing exhibit an apparent yielding effect during the polishing course, which contributes to the achievement of plastic flow removal for the wafer surface. The experimental results show that the surface roughness and subsurface damage of the sapphire wafer polished by the flexible polishing process can be decreased by 18.7% and 57.3%, respectively, compared with those of the sapphire wafer polished by the rigid polishing process.