The numerical simulation of a Mach 2.0 scaled supersonic experimental airplane is conducted with the consideration of the integration between air-frame and engine nacelles. A three-dimensional Euler CFD (Computational Fluid Dynamics) code with an overset-grids technique is adopted for solving the flow-field around a complex airplane configuration. The calculated pressure distributions were compared with wind tunnel test data and showed good agreement with them. The aerodynamic design tool, which combines the CFD code with an optimization technique for drag minimization, was developed. At first, it is applied to an axisymmetrical body in order to validate this design tool. The result showed that the optimized body geometry agrees well with the Sears-Haack body. Next, it was applied to two bodies under a wing-body configuration. The pressure drag of the optimized configurations was about 9 percent lower than that of the Sears-Haack body and their final volumes were maintained at the initial volume.