The unsteady flow field around a moving airfoil section was obtained by solving the Euler equation. The CUDA programming language was used to provide a parallel computing capacity on GPU. The ARMA(auto-regressive-moving-average) model was used to identify the unsteady aerodynamic forces, and simulation results using the identified aerodynamic model of the system identification agree well with those using the full ordered CFD model. Furthermore, the transonic flutter of the Isogai Wing with an Stype flutter boundary, which is the standard example in aero-elasticity, was calculated. The approach presented can greatly improve the efficiency of computing without loss of accuracy.