The authors’ previous research developed a medium-fidelity aeroelastic analysis scheme which could estimate drag coefficients for morphing wings. In the scheme, mainly the vortex lattice method and the finite element method are combined to capture the aeroelastic behavior of morphing wings, and a 2D CFD code is used to estimate the parasite drag coefficient. Although this method is efficient in terms of the analysis cost, the precision of the analysis tool remains to be verified. This study combines a 3D CFD code with the finite element method, and the drag estimation of the middle-fidelity aeroelastic analysis scheme is evaluated through the comparison with that of the higher-fidelity analysis scheme.