Due to the large size and small stiffness of aircraft skin, it is easy to produce machining deformation during cutting processing. Aiming at the problem of mirror machining deformation of skin, a deformation prediction flexible method based on substructure technology is proposed. This method divides the whole thin-walled part into two parts, and reduces difficulty of solving the deformation model of the whole thin-walled part by coupling the deformation models of the two parts. On the basis of considering the continuity of tool path deformation, the traditional iterative method is still used to predict machining deformation at the initial cutting position while in other cutting positions, convergence depth of the previous cutting position is used as the initial iterative value. Compared with the traditional iterative prediction method of machining deformation, the proposed method greatly improves the convergence rate. Moreover, effectiveness of the proposed method was demonstrated through finite element simulation and mirror machining experiments, with overall computational time and iteration times reduced by 46.15% and 41.94%, respectively.