The problems of uncertainty modeling and model validation of aeroelastic system are investigated. The parametric uncertainty is considered to denote the uncertainties in structure, and both parametric form and unmodeled dynamics are used to represent the influences and mechanism of uncertainties in unsteady aerodynamic forces. The Linear Fractional Transformation representation of the uncertain aeroelastic system is established to perform model validation and robust flutter analysis. A testing method for the existence of a validating model set in frequency-domain is developed, then the model validating sets are parameterized and the problem of searching the uncertainty magnitudes can be formulated as an optimization process. The influence of exogenous disturbances and noise, which are inevitable in actual testing environment and commonly unknown but energy bounded is considered, and consequently the conservatism of the uncertainty bounds is reduced. At last, for the uncertain aeroelastic system with the obtained uncertainty magnitudes, the robust flutter analysis based on structured singular value theory is performed to predict the robust stability boundary. The comparison of the results associated with two different uncertainty descriptions and the influences of disturbance and noise are discussed. Two numerical examples are presented and the results of the simulation demonstrate the validity of the developed method