Time-varying dynamic behaviors are essential to investigate the stability in the thin-walled workpiece milling process, which is usually affected by material removal and position-dependent characteristics of the workpiece along with the tool feed direction. To predict the milling stability with position-dependent, thin-walled component multi-axis milling, an improved structural dynamic modification method with variable mass is proposed in the paper. Firstly, the extraction of multi-axis milling material and the removal process of thin-walled parts with a complex curved surface and variable thickness is completed with CAM software. Then, the material removal of one cutting path as a modification of the structure is divided into multi-cutting steps with equal length to obtain the corrected FRFs in the machining process on the basis of the extended Sherman-Morrison-Woodbury formula. Furthermore, the dynamic characteristics of the initial un-machined workpiece and final machined workpiece are calculated by both experimental modal analysis and FEM. Finally, the multi-axis milling stability is predicted using the extended numerical integrated method, and an aero-engine blade is used to validate the accuracy and effectiveness of the proposed method for multi-axis milling molding parts.