Aiming at the edge-milling distortion problem of the composite thin-walled workpiece, which is clamped on the flexible tooling system, the milling process is simulated by finite element method with commercial software ABAQUS. The influence of POGO column spacing, POGO column to edge margin, and the main fiber angle of composite thin-walled parts on the milling deformation is studied. A method for predicting the deformation of thin-walled parts during flexible clamping is proposed. This method can effectively predict the deformation of thin-walled parts under the influence of parameters such as spacing, margins, and angles. The method has a maximum error value of 3.6% for the prediction of the edge weight deformation of thin-walled parts, and a maximum error value of 2.70% for the prediction of the external force deformation of the edge of the thin-walled parts.