A deformation control method based on numerical simulation and process optimization is proposed to solve the problem of deformation deviation in Ti6Al4V titanium alloy vertical tail joints during shot peening strengthening for civil large aircraft. The deformation evolution law during shot peening process was systematically analyzed using Abaqus finite element discrete element (FEM-DEM) coupled simulation technology. The experiment used two sets of complete grade parts for comparative study: the first group examined the influence of different shot peening pressure parameters (0.16 and 0.23 MPa), and the second group evaluated the support effect of flexible polyurethane pads. Using a high-precision CNC coordinate measuring machine, the vector deviation values of 38 characteristic coordinate points on the profile of each test piece were analyzed to verify the deformation effect of two sets of experiments on the Ti6Al4V titanium alloy vertical tail joint. The results show that the shot peening process with internal and external strength difference can significantly reduce deformation by up to 0.2 mm compared to traditional isostatic shot peening; Using customized flexible support pads to further reduce local deformation by 0.1 mm; The FEM-DEM coupling model accurately predicted the maximum deformation position, and the combination of model simulation and process optimization can effectively control the deformation of Ti6Al4V titanium alloy vertical tail joints.