A folding wing aircraft can autonomously change its configuration in flight to respond to different flying environments. Hinge moment during morphing process is an important basis for driving mechanism design and structural strength check, and its calculation depends on the simulation of the morphing process. Existing studies mostly use the simplified lifting surface method for aerodynamic modeling. In this paper, the CFD-based simulation method is studied, and the results are compared with those by the lifting surface method. First, the unsteady aerodynamic modeling method of the folding wing based on the CFD method is studied, an effective description method is given to define the wall mesh motion caused by wing folding and aileron deflection, and an unfolding–refolding strategy is proposed to improve the quality of the internal mesh in the case of large folding angles. Then, the CFD aerodynamic model is coupled through a developed coupling calculation program with the flexible multibody structure model for the simulation of a flight-morphing process. The comparison with the results of the lifting surface method shows that hinge moments obtained according to the two aerodynamic models are markedly different. Analysis of the difference shows that airfoil thickness considerably affects aerodynamic loading distributions and hinge moments of folding wing aircraft. The lifting surface method ignores airfoil thickness, which will cause large simulation errors in hinge moments.