This paper describes the modeling data and final analysis results of rotor resonance, rotor aeroelastic stability and whirl flutter stability for Smart UAV (SUAV). The effects of wing beamwise, chordwise and torsional stiffness on the whirl flutter stability were investigated considering the possibility of design change of SUAV wing structure. The parametric study showed that wing torsional and beamwise stiffness changes have much stronger influence on the wing mode damping than chordwise stiffness. It was analytically demonstrated that the final designed rotor system is aeroelastically stable and free from resonance, and that rotor/pylon/wing system of SUAV TR-S4 has enough rotor stability and whirl flutter stability margin.