A nonlinear aeroelastic analysis system has been developed using the coupled numerical techniques of computational fluid dynamics (CFD) and computational structural dynamics (CSD) in the present study and the analysis system has been applied to an actual aircraft design procedure to examine aeroelastic stabilities. An aerodynamic analysis is performed using the transonic small disturbance (TSD) theory for computational efficiency and the results are compared with experimental data. An aeroelastic analysis in the time domain is performed to obtain the flutter boundaries of the aircraft model. Finally, the various effects of launchers and control surfaces are investigated.