Unmanned aerial vehicles (UAVs) with folding wings can serve in multiple mission profiles, usually accompanied by sudden changes in flight speed. These bring great challenges to the aeroelastic design of UAVs, especially in the calculation of flutter characteristics. This paper developed a new non-intrusive aeroelastic model to quickly calculate the flutter characteristics of Z-shaped folding wings at different folding angles. First, the original Z-shaped folding wing was designed to be enhanced. Beams and ribs were arranged inside each wing segment to enhance the structural strength performance. Control surfaces were arranged in the middle-wing and outer-wing to enhance the aerodynamic control performance. Second, a parametric aeroelastic model at any folding angle was reconstructed based on the input file of Nastran software for the flutter calculation of the folding wing in the unfolded state. Finally, the effects of parameters such as folding angle, hinge stiffness between different wing segments, and hinge stiffness of the control surfaces on the flutter characteristics of the folding wing were investigated. The results show that the enhancement scheme could significantly increase the flutter speed and flutter frequency of the folding wing. The hinge stiffness between each wing segment had a significant impact on the flutter characteristics of the folding wing, but flutter at the control surface basically did not occur.