Abstract: Transonic flutter simulation and transonic flutter wind tunnel test are the main techniques in the design process for the high maneuver aircraft. In this paper, the finite element method (FEM) based modal analysis, flutter calculation using doublet lattice method (DLM), and the transonic flutter simulation by CFD method are carried out for the structural similar flutter mode of a whole aircraft. The transonic flutter wind tunnel test is accomplished in FL-26 wind tunnel. By correlation analysis of the results by the numerical simulation with those of the wind tunnel test, a complex flutter mode of the whole aircraft is investigated and verified. The effectiveness and the accuracy of the Navier-Stokes equations based transonic CFD code with hybrid mesh are verified, and it shows the progress we have made on the unsteady aerodynamic CFD simulation of aircraft. Combining transonic flutter wind tunnel test with CFD simulation, the complex coupling flutter design for the whole aircraft could be accomplished.