The body freedom flutter characteristics of an airfoil and a fly wing aircraft model were calculated based on a CFD method for the Navier–Stokes equations. Firstly, a rigid elastic coupling dynamic model of a two-dimensional airfoil with a free–free boundary condition was derived in an inertial frame and decoupled by rigid body mode and elastic mode. In the fluid–solid coupling method, the rigid body was trimmed by subtracting the generalized steady aerodynamic force from the structural dynamic equation. The flutter characteristics were predicted by the variable stiffness method at a fixed Mach number and flight altitude. Finally, validation of the predicted body freedom flutter characteristics was performed through a comparison of theoretical solutions based on a Theodorsen unsteady aerodynamic model for airfoil and experimental results for a fly wing aircraft model. The mechanism of the influence of the bending mode stiffness and the position of the center of gravity on the body freedom flutter characteristics were briefly analyzed.