The transport aircraft experience frequently higher loads than what are designed for, in particular, in unusual flight conditions, such as encountering severe atmospheric turbulence, sudden evasive motion in avoiding air collision, and hard landings. The structural damage, fatigue cracking, or non-typical structural deformation may be caused by these high loads. This paper will present a method based on the concept of aeroelastic effects on stability and control derivatives to indirectly determine the structural integrity of transport aircraft. Aerodynamic models are established through fuzzy-logic modeling (FLM) of the flight data extracted from quick access recorder (QAR). Stability and control derivatives with static aeroelastic effects are then estimated by using these aerodynamic models. Qualitative evaluation of the aeroelastic effects on the wing and tail is based on the second derivatives of normal force and pitching moment coefficients with the angle of attack and dynamic pressure, respectively. A twin-jet transport aircraft encountered severe atmospheric turbulence with a sudden plunging motion in revenue flight as the study case. The comparative analysis of aeroelastic effects for this twin-jet transport before and during severe atmospheric turbulence will be illustrated in this paper.