Owing to reliability and high strength-to-weight ratio, large thin-walled components are widely used in the aviation and aerospace industry. Due to the complex features and sequence involved in the machining process of large thin-walled components, machining deformation of com-ponent is easy to exceed the specification. In order to address the problem, it is important to retain the appropriate finishing allowance. To find the overall machining deformation, finishing allowance-induced deformation (web finishing allowance, sidewall finishing allowance) and initial residual stress-induced deformation were considered as major factors. Meanwhile, machined sur-face residual stress-induced deformation, clamping stress-induced deformation, thermal deforma-tion, gravity-induced deformation and inertial force-induced deformation were neglected in the optimization model. Six-peak Gaussian function was introduced to fit the initial residual stress. Based upon the obtained function of initial residual stress, a deformation prediction model between initial residual stress and finishing allowance was established to attain the finishing allowance-induced deformation. In addition, linear programming optimization model based on the simplex algorithm was developed to optimize the overall machining deformation. Results have concluded that the overall machining deformation reached the minimum value when sidewall finishing allow-ance and web finishing allowance varied between 1 and 2 mm. Additionally, web finishing allowance-induced deformation and sidewall finishing allowance-induced deformation were 1.05 mm and 0.7 mm. Furthermore, the machining deformation decreased to 0.3–0.38 mm with the application of optimized finishing allowance allocation strategy, which made 39–56% reduction of the overall machining deformation compared to that in conventional method.