Variations in system parameters due to uncertainties of parameters may result in system performance deterioration and create system internal stability problems. Uncertainties in structural modeling of structures are often considered to ensure that the control system is robust with respect to response errors. So the uncertain concept plays an important role in the analysis and design of the engineering structures. In this paper, the active control of the intelligent structures with the uncertainties is studied and a new method for analyzing the robustness of systems with the uncertainties is presented. Firstly, the system with uncertain parameters is considered as the perturbation of the system with deterministic parameters. Secondly, the feedback control law is designed on the basis of deterministic system. Thirdly, perturbation analysis and robustness analysis of intelligent structures with uncertainties are discussed when the feedback control law is applied to the original system and perturbed system. Combining the convex model of uncertainties with the finite element method, the analysis theory of the robustness of intelligent structures with the uncertainties can be developed. The description and computation of the robustness of intelligent structures with uncertain parameters is obtained. Finally, a numerical example of the application of the present method is given to show the validity of the method.