Thin anisotropic crystals (TACs) have potential applications in semiconductors, microelectronics, and aerospace. However, polishing a TAC workpiece with a compliant tool is highly challenging because of its susceptibility to deformation and brittle damage owing to its thin structure. Another significant challenge for polishing is the anisotropic discrepancy, which is highly dependent on the crystal planes/directions. To address these challenges and ultimately realize the process control of polishing a TAC workpiece, this study establishes a comprehensive multiscale modeling framework. The proposed framework analytically incorporates the macroscale tool–TAC interaction mechanics, macro/micro coupling material removal mechanism, and macro/micro coupling subsurface damage behavior according to the physical properties of a TAC workpiece. Experiments at different scales are conducted to validate notable discrepancies in the surface and subsurface material responses in the polishing of a TAC workpiece, agreeing well with analytical predictions. Based on the cross-scale study and framework, space- and time-domain control strategies are proposed, demonstrating the capability for effectively eliminating the anisotropic discrepancy from macro- to microscale and enabling deterministic control in the polishing of TACs.