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This paper builds an aerodynamic optimization design system by coupling the free form deformation parameterization technique, the dynamic mesh technique based on inverse distance weighting interpolation method and particle swarm optimization algorithm, Kriging surrogate model, with the computational fluid dynamics solver based on Reynolds-averaged Navier–Stokes equations. And it carries out aerodynamic optimization designs with a supersonic transport aircraft configuration. The wing shape is parameterized by defining 60 design variables and the wing twist is by four design variables. Meanwhile, the wing thickness constraints are considered. Afterwards, a single-point optimization design aiming at minimum of the supersonic cruise drag is conducted, and in order to consider the transonic cruise condition, a multipoint aerodynamic optimization design aiming at minimum of a weighted drag for the supersonic cruise drag and transonic cruise drag is performed. The analyses of optimization results illustrate the specific drag reduction, the characteristics of pressure distributions for both the supersonic cruise condition and transonic cruise condition, and how the shock wave region and strength have improved on the supersonic cruise condition. The optimization design this paper presents realizing the drag reduction is quite practical and effective, which is instructive in supersonic aircraft design.