The Radial Basis Function (RBF) method with data reduction is an effective way to perform mesh deformation. However, for large deformations on meshes of complex aerodynamic configurations, the efficiency of the RBF mesh deformation method still needs to be further improved to fulfill the demand of practical application. To achieve this goal, a multistep RBF method based on a multilevel subspace RBF algorithm is presented to further improve the efficiency of the mesh deformation method in this research. A whole deformation is divided into a series of steps, and the supporting radius is adjusted in accordance with the maximal displacement error. Furthermore, parallel computing is applied to the interpolation to enhance the efficiency. Typical deformation problems of the NASA Common Research Model (CRM) configuration, the DLR-F6 wing-body-nacelle-pylon configuration, and the DLR-F11 high-lift configuration are tested to verify the feasibility of this method. Test results show that the presented multistep RBF mesh deformation method is efficient and robust in dealing with large deformation problems over complex geometries.