Many of the aerospace components are characterized by having pocket-shaped thin-walled structures. During milling, the varying dynamics of the workpiece due to the change of thickness affects the final part quality. Available dynamic models rely on computationally prohibitive techniques that limit their use in the aerospace industry. In this paper, a new dynamic model was developed to predict the vibrations of thin-walled pocket structures during milling while taking into account the continuous change of thickness. The model is based on representing the change of thickness of a pocket-structure with a two-directional multispan plate. For the model formulation, the Rayleigh–Ritz method is used together with multispan beam models for the trial functions in both the x- and y-directions. An extensive finite element (FE) validation of the developed model was performed for different aspect ratios of rectangular and nonrectangular pockets and various change of thickness schemes. It was shown that the proposed model can accurately capture the dynamic effect of the change of thickness with prediction errors of less than 5% and at least 20 times reduction in the computation time. Experimental validation of the models was performed through the machining of thin-walled components. The predictions of the developed models were found to be in excellent agreement with the measured dynamic responses.