Mesh deformation method based on radial basis function (RBF) is a reliable technique to be used to obtain high-quality deformed mesh for arbitrary topology. Reduced control points method can greatly improve the efficiency of the mesh deformation, while there exists the problem of large deformation error on surface and inverted boundary layer mesh. In this paper a new mesh deformation method with viscous boundary layer mesh is developed. The method selects two groups of control points from the object surface, a set of control points to roughly calculate grid position and deformation error, and the second set of control points to get a more accurate deformed mesh with interpolation deformation error. Mesh deformation of NLR-7301 with flap and DLR-F6 wing-body-pylon-nacelle configuration is presented with the viscous mesh deformation method. Results show that the method can greatly reduce deformation error on surface and effectively avoid boundary layer mesh inverted.