During the milling of thin-walled blades, the removal of material exhibits strong time-varying dynamics, leading to chatter and a decrease in surface quality. To address the issue of milling vibrations in the machining of complex thin-walled blades used in aerospace applications, this work proposes a process optimization approach involving non-uniform allowances. The objective is to enhance of he stiffness of the thin-walled parts during the milling process by establishing a non-uniform allowance distribution for the finishing process of thin-walled blades. By applying the theory of sensitive process stiffness and conducting finite element simulations, two processing strategies, namely uniform allowances and non-uniform allowances, are evaluated through cutting experiments. The experimental results demonstrate that the non-uniform allowance processing strategy leads to a more evenly distributed acceleration spectrum and a 50% reduction in amplitude. Moreover, the surface exhibits no discernible vibration pattern, resulting in a 35% decrease in roughness. The non-uniform allowance-processing strategy proves to be effective in significantly improving the rigidity of the thin-walled blade processing system, thereby enhancing the stability of the cutting process. These findings hold significant relevance in guiding the machining of typical complex thin-walled aerospace components.