In this study, transonic aeroelastic response analyses have been conducted for the DLR-F4(wing-body) aircraft configuration considering shockwave and flow separation effects. The developed fluid-structure coupled analysis system is applied for aeroelastic computations combining computational structural dynamics(CSD), finite element method(FEM) and computational fluid dynamics(CFD) in the time domain. It can give very accurate and useful engineering data on the structural dynamic design of advanced flight vehicles. For the nonlinear unsteady aerodynamics in high transonic flow region, Navier-Stokes equations using the structured grid system have been applied to wing-body configurations. In transonic flight region, the characteristics of static and dynamic aeroelastic responses have been investigated for a typical wing-body configuration model. Also, it is typically shown that the current computation approach can yield realistic and practical results for aircraft design and test engineers.