In the aircraft design, a careful consideration of aeroelastic stability is very important because the aeroelastic instabilities cause the aircrafts to have structural failure in a short time. 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. The analysis system has been applied to examine the aeroelastic stabilities on the actual aircraft design. The aerodynamic anayses are performed using the transonic small disturbance (TSD) theory for computational efficiency and the results are compared with exterimental data. The aeroelastic anayses in the time domain are performed to obtain the flutter boundaries of the aircraft model. The various effects of launchers and control surfaces are investigated.