Aircraft skin is a critical external structural component that provides aerodynamic profile, sustains and transfers aerodynamic loads, and protects internal systems from harsh environments. High machining precision is essential to ensure assembly accuracy and flight performance. However, large scale thin walled skin components are prone to significant machining deformation due to their low stiffness. Traditional deformation control methods, which relying heavily on experiments and full-process simulations, are inefficient and costly for industrial applications. To address this issue, this paper establishes a correlation model among machining parameters, residual stress, equivalent bending moment, and machining deformation. Single-factor experiments are conducted to reveal the effects of spindle speed, feed rate, and cutting depth on surface residual stress. Based on plate-shell theory, the relationship between residual stress and equivalent bending moment is established. The quantitative relationship between equivalent bending moment and machining deformation of the skin is obtained via finite element simulation modeling. Finally, a deformation control strategy for the skin during finish machining is established by optimizing the cutting depth. Experimental results show that after parameter optimization, the overall machining deformation of the 5A06 aluminum alloy skin is reduced by 81%, and the maximum deformation is controlled within 0.17 mm, which fully meets the aeronautical assembly requirements. This work provides an efficient and low-cost process optimization strategy for the machining deformation control of large weak-stiffness thin-walled components.