The stiffness of boundary conditions in mechanical structures is difficult to represent. A method is proposed to model the mechanical performance of the clamped boundary condition based on thin-layer element. Firstly, the contact surface of clamped boundary condition is parameterized by using isotropic thin-layer element to model the normal and tangential contact stiffness. Secondly, material parameter of thin-layer element is identified by using experimental modal data, parameter identification is transformed as an optimization problem. Experimental investigation is undertaken to verify the proposed method by employing an aluminum honeycomb panel, the numerical model of which is constructed by using the equivalent theory. Thin-layer elements with different properties are used to simulate the mechanical properties in different area of the boundary conditions, and the experimental modal data is adopted to identify the material parameters. Results show that the width to thickness ratio of the thin layer element has a great influence on the identification results.